44 Works

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...

Data from: Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

Daniel S. Karp, Rebecca Chaplin-Kramer, Timothy D. Meehan, Emily A. Martin, Fabrice DeClerck, Heather Grab, Claudio Gratton, Lauren Hunt, Ashley E. Larsen, Alejandra Martínez-Salinas, Megan E. O’Rourke, Adrien Rusch, Katja Poveda, Mattias Jonsson, Jay A. Rosenheim, Nancy A. Schellhorn, Teja Tscharntke, Stephen D. Wratten, Wei Zhang, Aaron L. Iverson, Lynn S. Adler, Matthias Albrecht, Audrey Alignier, Gina M. Angelella, Muhammad Zubair Anjum … & Yi Zou
The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are...

Data from: Estimating range expansion of wildlife in heterogeneous landscapes: a spatially explicit state-space matrix model coupled with an improved numerical integration technique

Yutaka Osada, Takeo Kuriyama, Masahiko Asada, Hiroyuki Yokomizo & Tadashi Miyashita
Dispersal as well as population growth is a key demographic process that determines population dynamics. However, determining the effects of environmental covariates on dispersal from spatial-temporal abundance proxy data is challenging owing to the complexity of model specification for directional dispersal permeability and the extremely high computational loads for numerical integration. In this paper, we present a case study estimating how environmental covariates affect the dispersal of Japanese sika deer by developing a spatially explicit...

Data from: Personality links with lifespan in chimpanzees

Drew M Altschul, William D Hopkins, Elizabeth S Herrelko, Miho Inoue-Murayama, Tetsuro Matsuzawa, James E King, Stephen R Ross & Alexander Weiss
Life-history strategies for optimizing individual fitness fall on a spectrum between maximizing reproductive efforts and maintaining physical health over time. Strategies across this spectrum are viable and different suites of personality traits have evolved to support these strategies. Using personality and survival data from 538 captive chimpanzees (Pan troglodytes) we tested whether any of the dimensions of chimpanzee personality - agreeableness, conscientiousness, dominance, extraversion, neuroticism, and openness - were associated with longevity, an attribute of...

Data from: Catch diversification provides multiple benefits in inland fisheries

Shin-Ichiro S. Matsuzaki, Ryuichiro Shinohara, Kei Uchida & Takehiro Sasaki
1. Diversification of fisheries and agroecosystems can increase and stabilize production and revenue, despite unpredictable changes in ecosystems and markets. Recent work suggests that diversification can provide multiple benefits simultaneously, but empirical evidence of relationships between catch or crop diversification and the provision of multiple benefits is scarce. The effect of diversification on multiple benefits may vary temporally and among systems. 2. Using long-term (11–54 years) capture fishery statistics from five Japanese lakes, we examined...

Relational values help explain green infrastructure preferences: The case of managing crane habitat in Hokkaido, Japan

Hyerin Kim, Yasushi Shoji, Takahiro Tsuge, Takahiro Kubo & Futoshi Nakamura
The initial purpose of our study was to understand preferences of stakeholders on green infrastructure for flood control using a discrete choice experiment. However, the results of our study included unexpected findings. According to the utility theory of economics, an inexpensive green infrastructure scenario should have been chosen under ceteris paribus conditions, but our results differed from this expectation. Inconsistent results like ours are often interpreted as indicating bias and/or questionnaire design issues. However, our...

TCCON data from Saga (JP), Release GGG2020.R0

K. Shiomi, S. Kawakami, H. Ohyama, K. Arai, H. Okumura, H. Ikegami & M. Usami
The Total Carbon Column Observing Network (TCCON) is a network of ground-based Fourier Transform Spectrometers that record direct solar absorption spectra of the atmosphere in the near-infrared. From these spectra, accurate and precise column-averaged abundances of atmospheric constituents including CO2, CH4, N2O, HF, CO, H2O, and HDO, are retrieved. This is the GGG2020 data release of observations from the TCCON station at Saga, Japan

Data from: Mixed mating system are regulated by fecundity in Shorea curtisii (Dipterocarpaceae) as revealed by comparison under different pollen limited conditions

Naoki Tani, Yoshihiko Tsumura, Keita Fukasawa, Tomoyuki Kado, Yuriko Taguchi, Soon Leong Lee, Chai Ting Lee, Norwati Muhammad, Kaoru Niiyama, Tatsuya Otani, Tsutomu Yagihashi, Hiroyuki Tanouchi, Azizi Ripin & Abdul Rahman Kassim
The maintenance of mixed mating was studied in Shorea curtisii, a dominant and widely distributed dipterocarp species in Southeast Asia. Paternity and hierarchical Bayesian analyses were used to estimate the parameters of pollen dispersal kernel, male fecundity and self-pollen affinity. We hypothesized that partial self incompatibility and/or inbreeding depression reduce the number of selfed seeds if the mother trees receive sufficient pollen, whereas reproductive assurance increases the numbers of selfed seeds under low amounts of...

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: A shady phytoplankton paradox: when phytoplankton increases under low light

Masato Yamamichi, Takehiro Kazama, Kotaro Tokita, Izumi Katano, Hideyuki Doi, Takehito Yoshida, Nelson Hairston, Jotaro Urabe & Nelson G. Hairston
Light is a fundamental driver of ecosystem dynamics, affecting the rate of photosynthesis and primary production. In spite of its importance, less is known about its community-scale effects on aquatic ecosystems compared with those of nutrient loading. Understanding light limitation is also important for ecosystem management, as human activities have been rapidly altering light availability to aquatic ecosystems. Here we show that decreasing light can paradoxically increase phytoplankton abundance in shallow lakes. Our results, based...

Data from: The potential role of temperate Japanese regions as refugia for the coral Acropora hyacinthus in the face of climate change

Aki Nakabayashi, Takehisa Yamakita, Takashi Nakamura, Hiroaki Aizawa, Yuko F. Kitano, Akira Iguchi, Hiroya Yamano, Satoshi Nagai, Sylvain Agostini, Kosuke M. Tshima & Nina Yasuda
As corals in tropical regions are threatened by increasing water temperatures, poleward range expansion of reef-building corals has been observed, and temperate regions are expected to serve as refugia in the face of climate change. To elucidate the important indicators of the sustainability of coral populations, we examined the genetic diversity and connectivity of the common reef-building coral Acropora hyacinthus along the Kuroshio Current, including recently expanded (<50 years) populations. Among the three cryptic lineages...

Highly mobile seed predators contribute to interisland seed dispersal within an oceanic archipelago

Haruko Ando, Yuka Mori, Miho Nishihiro, Kanon Mizukoshi, Masaki Akaike, Wataru Kitamura & Nozomu J. Sato
Long-distance dispersal (LDD) is an essential event for species colonization and expansion in oceanic island ecosystems. Endozoochory by birds is an important factor promoting the LDD of plant seeds, but its contribution to interisland seed dispersal is still unclear. Here, we show possible seed dispersal by a seed predator pigeon, the Japanese wood pigeon Columba janthina, among oceanic islands in the Izu archipelago, Japan. Although some previous studies showed that most seeds swallowed by this...

Nitrogen budget data

Tan Zou, Xin Zhang, Luis Lassaletta, Nathaniel Mueller, Francesco Tubiello, Matthew Lisk, Chaoqun Lu, Richard Conant, Christopher Dorich, James Gerber, Hanqin Tian, Tom Bruulsema, Tai Maaz, Kazuya Nishina, Benjamin Bodirsky, Alexander Popp, Lex Bouwman, Arthur Beusen, Jinfeng Chang, Petr Havlík, David Leclère, Josep Canadell, Robert Jackson, Patrick Heffer, Nathan Wanner … & Eric Davidson
Input-output estimates of nitrogen (N) on cropland are essential for improving N management and better understanding the global N cycle. Here, we compare 13 N budget datasets covering 115 countries and regions over 1961-2015. Though most datasets showed similar spatiotemporal patterns, some annual estimates varied widely among them, resulting in large ranges and uncertainty. In 2010, global medians (in Tg N yr-1) and associated min-max ranges were 73 (64-84) for global harvested crop N; 161...

Data from: Intraspecific variations in life history traits of two pecky rice bug species from Japan: mapping emergence dates and number of annual generations

Kazuhisa Yamasaki, Ken Tabuchi, Akihiko Takahashi, Takeshi Osawa, Akira Yoshioka, Yasushi Ishigooka, Shigeto Sudo & Mayura Takada
The mirid bugs Stenotus rubrovittatus and Trigonotylus caelestialium, which cause pecky rice, have become a threat to rice cultivation in Asia. Damage caused by these pests has rapidly become frequent since around 2000 in Japan. Their expansion pattern is not simple, and predicting their future spread remains challenging. Some insects with wide ranges have locally adapted variations in life-history traits. We performed laboratory rearing experiments to assess the geographical scale of intraspecific variations in life-history...

Dataset and R code from: Positive and negative effects of land abandonment on butterfly communities revealed by a hierarchical sampling design across climatic regions

Keita Fukasawa, Naoki Sugimoto, Akio Asahara, Minoru Kasada, Misako Matsuba & Tadashi Miyashita
Land abandonment may decrease biodiversity but also provides an opportunity for rewilding. It is therefore necessary to identify areas that may benefit from traditional land management practices and those that may benefit from a lack of human intervention. In this study, we conducted comparative field surveys of butterfly occurrence in abandoned and inhabited settlements in 18 regions of diverse climatic zones in Japan to test the hypotheses that species-specific responses to land abandonment correlate with...

Data from: Underlying geology and climate interactively shape climate change refugia in mountain streams

Nobuo Ishiyama, Masanao Sueyoshi, Jorge Garcia Molinos, Kenta Iwasaki, Junjiro N Negishi, Itsuro Koizumi, Shigeya Nagayama, Akiko Nagasaka, Yu Nagasaka & Futoshi Nakamura
Identifying climate-change refugia is a key adaptation strategy for reducing global warming impacts. Knowledge of the effects of underlying geology on thermal regime along climate gradients and the ecological responses to the geology-controlled thermal regime is essential to plan appropriate climate adaptation strategies. In the present study, the dominance of volcanic rocks in the watershed is used as a landscape-scale surrogate for cold groundwater inputs to clarify the importance of underlying geology in stream ecosystems...

Data from: Recovery of macrobenthic communities in tidal flats following the Great East Japan Earthquake

Jotaro Urabe, Takeshi Yuhara, Takao Suzuki, Tatsuki Nishita, Junichi Murakami, Wataru Makino, , Kyoko Kinoshita, Natsuru Yasuno & Takashi Uchino
Extreme geo-climatic events can occur everywhere in the world. The Great East Japan Earthquake, with a moment magnitude scale of 9.0 M on March 11, 2011, was one of these events and caused huge tsunamis that changed largely tidal communities on the Pacific coast of eastern Japan. However, subsequent long-term changes in the communities after such an extreme geo-climatic event have rarely been examined. Therefore, we performed the biological monitoring over a ten-year span, before...

Estimation of breeding population size using DNA-based pedigree reconstruction in brown bears

Michito Shimozuru, Mina Jimbo, Keisuke Adachi, Kei Kawamura, Yuri Shirane, Yoshihiro Umemura, Tsuyoshi Ishinazaka, Masanao Nakanishi, Mayu Kiyonari, Masami Yamanaka, Yukihiro Amagai, Ayaho Ijuin, Tomoki Sakiyama, Shinsuke Kasai, Takane Nose, Masataka Shirayanagi, Hifumi Tsuruga, Tsutomu Mano, Toshio Tsubota, Keita Fukasawa & Hiroyuki Uno
Robust estimates of demographic parameters are critical for effective wildlife conservation and management, but are difficult to obtain for elusive species. We estimated the breeding and adult population sizes, as well as the minimum population size, in a high-density brown bear population on the Shiretoko Peninsula, in Hokkaido, Japan, using DNA-based pedigree reconstruction. A total of 1,288 individuals, collected in and around the Shiretoko Peninsula between 1998 and 2020, were genotyped at 21 microsatellite loci....

Data from: Mate choice for body size leads to size assortative mating in the Ryukyu Scops Owl Otus elegans

Akira Sawada, Tetsuya Iwasaki, Kana Akatani & Masaoki Takagi
Understanding evolutionary phenomena that involve size assortative mating, requires elucidating the generating mechanisms on which assortment is based. Although various mechanisms have been suggested, their relative importance may differ across taxonomic groups. Males selecting for large, fecund females combined with the dominance of large males in the competition for females, has been suggested as a major mechanism in specific groups. However, raptors do not appear to conform to this, because the selection for smallness among...

Registration Year

  • 2022
  • 2021
  • 2020
  • 2019
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  • 2015
  • 2013
  • 2010

Resource Types

  • Dataset


  • National Institute for Environmental Studies
  • University of Tokyo
  • Hokkaido University
  • Tohoku University
  • Kyoto University
  • University of Minnesota
  • Azabu University
  • Hokkaido Research Organization
  • University of Tsukuba
  • Commonwealth Scientific and Industrial Research Organisation