18 Works

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...

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: 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: 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: 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: The effects of temporal and spatial predictions on stretch reflexes of ankle flexor and extensor muscles while standing

Kimiya Fujio, Hiroki Obata, Noritaka Kawashima & Kimitaka Nakazawa
The purpose of the present study was to investigate how stretch reflex (SR) responses in the ankle extensor (soleus: SOL) and flexor (tibialis anterior: TA) muscles would be modulated with temporal and/or spatial predictions of external perturbations and whether their effects are specific to the standing posture. SR responses in the SOL/TA were elicited by imposing quick ankle toes-up/toes-down rotations while standing upright and in the supine position. We designed four experimental conditions based on...

Data from: Grouping substitution types into different relaxed molecular clocks

Hui-Jie Lee, Hirohisa Kishino, Nicolas Rodrigue & Jeffrey L. Thorne
Different types of nucleotide substitutions experience different patterns of rate change over time. We propose clustering context-dependent (or context-independent) nucleotide substitution types according to how their rates change and then using the grouping for divergence time estimation. With our models, relative rates among types that are in the same group are fixed, whereas absolute rates of the types within a group change over time according to a shared relaxed molecular clock. We illustrate our procedure...

Data from: Inbreeding avoidance and female mate choice shape reproductive skew in capuchin monkeys (Cebus capucinus imitator)

Eva C. Wikberg, Katherine M. Jack, Linda M. Fedigan, Fernando A. Campos, Akiko S. Yahsima, Mackenzie L. Bergstrom, Tomohide Hiwatashi, Shoji Kawamura, Katharine M. Jack & Akiko S. Yashima
Reproductive skew in multimale groups may be determined by the need for alpha males to offer reproductive opportunities as staying incentives to subordinate males (concessions), by the relative fighting ability of the alpha male (tug-of-war) or by how easily females can be monopolized (priority-of-access). These models have rarely been investigated in species with exceptionally long male tenures, such as white-faced capuchins, where female mate choice for novel unrelated males may be important in shaping reproductive...

Data from: Population structure and persistence of Pacific herring following the Great Tohoku earthquake

Shuichi Kitada, Ryohei Yoshikai, Tomonari Fujita, Katsuyuki Hamasaki, Reiichiro Nakamichi & Hirohisa Kishino
We evaluated the effect of the Great Tohoku earthquake, which occurred on March 11, 2011 in Japan, on the genetic diversity and population structure of Pacific herring (Clupea pallasii). Pacific herring (n = 4466) were collected between 2003 and 2014 through more than 20 sampling events during spawning periods at nine spawning sites throughout the Pacific herring distribution range in Japan. We measured them and genotyped 3784 fish at five microsatellite loci. Following the tsunami,...

Data from: Effects of light environment during growth on the expression of cone opsin genes and behavioral spectral sensitivities in guppies (Poecilia reticulata)

Yusuke Sakai, Hajime Ohtsuki, Satoshi Kasagi, Shoji Kawamura & Masakado Kawata
Background: The visual system is important for animals for mate choice, food acquisition, and predator avoidance. Animals possessing a visual system can sense particular wavelengths of light emanating from objects and their surroundings and perceive their environments by processing information contained in these visual perceptions of light. Visual perception in individuals varies with the absorption spectra of visual pigments and the expression levels of opsin genes, which may be altered according to the light environments....

Data from: Star-shaped trace fossil and Phymatoderma from Neogene deep-sea deposits in central Japan: probable echiuran feeding and fecal traces

Kentaro Izumi & Kazuko Yoshizawa
A co-occurrence of the ichnogenus Phymatoderma and a star-shaped horizontal trace fossil was discovered from Neogene deep-marine deposits (Misaki Formation, central Japan), and is described herein for the first time. Phymatoderma consists of a straight to slightly curved tunnel that shows first- or second-order branches. The tunnels are 5.30–27.25 mm in diameter and are filled with ellipsoidal pellets. The relatively well-preserved star-shaped trace fossil is a large horizontal structure (~18 cm×19 cm) that consists of...

Data from: Timescale- and sensory modality-dependency of the central tendency of time perception

Yuki Murai & Yuko Yotsumoto
When individuals are asked to reproduce intervals of stimuli that are intermixedly presented at various times, longer intervals are often underestimated and shorter intervals overestimated. This phenomenon may be attributed to the central tendency of time perception, and suggests that our brain optimally encodes a stimulus interval based on current stimulus input and prior knowledge of the distribution of stimulus intervals. Two distinct systems are thought to be recruited in the perception of sub- and...

Data from: Sperm allocation in relation to female size in a semelparous salmonid

Yuya Makiguchi, Masaki Ichimura, Takenori Kitayama, Yuuki Kawabata, Takashi Kitagawa, Takahito Kojima & Trevor E. Pitcher
To maximize reproductive success, males have to adaptively tailor their sperm expenditure in relation to the quality of potential mates because they require time to replenish their sperm supply for subsequent mating opportunities. Therefore, in mating contexts where males must choose among females in a short period of time, as is the case with semelparous species (which die after one intensely competitive short duration breeding season), selection on sperm allocation can be expected to be...

Data from: Genetic basis for variation in salinity tolerance between stickleback ecotypes

Makoto Kusakabe, Asano Ishikawa, Mark Ravinet, Kohta Yoshida, Takashi Makino, Atsushi Toyoda, Asao Fujiyama & Jun Kitano
Adaptation to different salinities can drive and maintain divergence between populations of aquatic organisms. Anadromous and stream ecotypes of threespine stickleback (Gasterosteus aculeatus) are an excellent model to explore the genetic mechanisms underlying osmoregulation divergence. Using a parapatric pair of anadromous and stream stickleback ecotypes, we employed an integrated genomic approach to identify candidate genes important for adaptation to different salinity environments. Quantitative trait loci (QTL) mapping of plasma sodium concentrations under a seawater challenge...

Data from: Flight paths of seabirds soaring over the ocean surface enable measurement of fine-scale wind speed and direction

Yoshinari Yonehara, Yusuke Goto, Ken Yoda, Yutaka Watanuki, Lindsay C. Young, Henri Weimerskirch, Charles-André Bost & Katsufumi Sato
Monitoring ocean surface winds is essential for understanding ocean and atmosphere interactions and weather forecasts. However, wind measured by satellite scatterometers and buoys are spatially and temporally coarse, particularly in coastal areas. We deployed small global positioning system units on soaring seabirds to record their tracks. Seabirds were accelerated by tail winds or slowed down by head winds during flight, so their flight speed changed in relation to wind speed and direction. Taking advantage of...

Data from: Energy expenditure of adult green turtles (Chelonia mydas) at their foraging grounds and during simulated oceanic migration

Manfred R. Enstipp, Katia Ballorain, Stéphane Ciccione, Tomoko Narazaki, Katsufumi Sato & Jean-Yves Georges
Measuring the energy requirements of animals under natural conditions and determining how acquired energy is allocated to specific activities is a central theme in ecophysiology. Turtle reproductive output is fundamentally linked with their energy balance so a detailed understanding of marine turtle energy requirements during the different phases of their life cycle at sea is essential for their conservation. We used the non-invasive accelerometry technique to investigate the activity patterns and energy expenditure (EE) of...

Data from: Evolutionarily stable disequilibrium: endless dynamics of evolution in a stationary population

Takeuchi Nobuto, Kunihiko Kaneko, Paulien Hogeweg & Nobuto Takeuchi
Evolution is often conceived as changes in the properties of a population over generations. Does this notion exhaust the possible dynamics of evolution? Life is hierarchically organized, and evolution can operate at multiple levels with conflicting tendencies. Using a minimal model of such conflicting multilevel evolution, we demonstrate the possibility of a novel mode of evolution that challenges the above notion: individuals ceaselessly modify their genetically-inherited phenotype and fitness along their lines of descent, without...

Data from: Variation in ligand responses of the bitter taste receptors TAS2R1 and TAS2R4 among New World monkeys

Kei Tsutsui, Masahiro Otoh, Kodama Sakurai, Nami Suzuki-Hashido, Takashi Hayakawa, Takumi Misaka, Yoshiro Ishimaru, Filippo Aureli, Amanda D. Melin, Shoji Kawamura & Hiroo Imai
Background: New World monkeys (NWMs) are unique in that they exhibit remarkable interspecific variation in color vision and feeding behavior, making them an excellent model for studying sensory ecology. However, it is largely unknown whether non-visual senses co-vary with feeding ecology, especially gustation, which is expected to be indispensable in food selection. Bitter taste, which is mediated by bitter taste receptors (TAS2Rs) in the tongue, helps organisms avoid ingesting potentially toxic substances in food. In...

Registration Year

  • 2016

Resource Types

  • Dataset


  • University of Tokyo
  • Tohoku University
  • Shizuoka University
  • University of Oslo
  • Hokkaido University
  • Fisheries Research Agency
  • National Institute of Genetics
  • University of Calgary
  • Japan Science and Technology Agency
  • Princeton University