42 Works

Data from: Amphibian chytridiomycosis in Japan: distribution, haplotypes, and possible entry into Japan

Koichi Goka, Jun Yokoyama, Yumi Une, Toshiro Kuroki, Kazutaka Suzuki, Miri Nakahara, Arei Kobayashi, Shigeki Inaba, Tomoo Mizutani & Alex Hyatt
A serious disease of amphibians caused by the chytrid fungus Batrachochytrium dendrobatidis was first found in Japan in December 2006 in imported pet frogs. This was the first report of chytridiomycosis in Asia. To assess the risk of pandemic chytridiomycosis to Japanese frogs, we surveyed the distribution of the fungus among captive and wild frog populations. We established a nested PCR assay that uses two pairs of PCR primers to amplify the internal transcribed spacer...

Data from: A cryptic Allee effect: spatial contexts mask an existing fitness–density relationship

Akira Terui, Yusuke Miyazaki, Akira Yoshioka & Shin-Ichiro S. Matsuzaki
Current theories predict that Allee effects should be widespread in nature, but there is little consistency in empirical findings. We hypothesized that this gap can arise from ignoring spatial contexts (i.e. spatial scale and heterogeneity) that potentially mask an existing fitness–density relationship: a ‘cryptic’ Allee effect. To test this hypothesis, we analysed how spatial contexts interacted with conspecific density to influence the fertilization rate of the freshwater mussel Margaritifera laevis. This sessile organism has a...

Data from: Predators regulate prey species sorting and spatial distribution in microbial landscapes

George Livingston, Kayoko Fukumori, Diogo Provete, Masanobu Kawachi, Noriko Takamura, Mathew Leibold & Mathew A. Leibold
1. The role of predation in determining the metacommunity assembly model of prey communities is understudied relative to that of interspecific competition among prey. Previous work on metacommunity dynamics of competing species has shown that sorting by habitat patch type and spatial patterning can be affected by disturbances. 2. Microcosms offer a useful model system to test the effect of multi-trophic interactions and disturbance on metacommunity dynamics. Here, we investigated the potential role of predators...

Data from: Asymmetric dispersal structures a riverine metapopulation of the freshwater pearl mussel Margaritifera laevis

Akira Terui, Yusuke Miyazaki, Akira Yoshioka, Kenzo Kaifu, Shin-Ichiro S. Matsuzaki & Izumi Washitani
Unidirectional water flow results in the downstream-biased, asymmetric dispersal of many riverine organisms. However, little is known of how asymmetric dispersal influences riverine population structure and dynamics, limiting our ability to properly manage riverine organisms. A metapopulation of the freshwater pearl mussel Margaritifera laevis may be sensitive to river currents because mussels are repeatedly exposed to downstream drift during floods—a parasitic life stage is the only, limited period (~40 days) during which larvae (glochidia) can...

Data from: Effect of canine oxytocin receptor gene polymorphism on the successful training of drug detection dogs

Akitsugu Konno, Miho Inoue-Murayama, Shinji Yabuta, Akiko Tonoike, Miho Nagasawa, Kazutaka Mogi & Takefumi Kikusui
Drug detection dogs can be trained to locate various prohibited drugs with targeted odors, and they play an important role in interdiction of drug smuggling in human society. Recent studies provide the interesting hypothesis that the oxytocin system serves as a biological basis for co-evolution between dogs and humans. Here, we offer the new possibility that genetic variation of the canine oxytocin receptor (OXTR) gene may regulate the success of a dog’s training to become...

Data from: Functional diversity promotes phytoplankton resource use efficiency

Lin Ye, Chun-Wei Chang, Shin-Ichiro S. Matsuzaki, Noriko Takamura, Claire E. Widdicombe & Chih-Hao Hsieh
1.Understanding the relationship between biodiversity and ecosystem functioning (BEF) is a central topic in ecology. Multi‐traits based functional diversity has been proposed to improve mechanistic understanding of the BEF relationship; however, how trait‐based functional diversity affects ecosystem functioning and processes has rarely been addressed in aquatic ecosystems. 2.Here, we examined the causal relationships between three phytoplankton functional diversity indices (FAD2, FDc, FRic) and Shannon diversity index versus resource use efficiency for nitrogen (RUEN), phosphorus (RUEP),...

High-resolution (1.3kmx1.3-km) WRF-Chem output driven with the Hestia, and two nightlight-based fossil fuel emission products over the LA basin from 5/15/2020-6/15/2020

S. Feng, T. Lauvaux, T. Oda, M.O. Román, Z. Wang, S. Maksyutov & V.L. Kalb
This high-resolution WRF-Chem model output is driven with three different fossil fuel emission products: Hestia (Gurney et al., 2018), and two nightlight-based CO2 emission data using the same setup as Feng et al (2016). The nightlight data products are based on DMSP (Oda and Maksyutov, 2011) and NASA’s Black Marble Nighttime Lights Product Suite (VNP46) (Román et al., 2018; Oda et al. 2020). This sensitivity atmospheric modeling experiment demonstrates the utility of CO2 mapping, helping...

Data from: Effectiveness of signs of activity as relative abundance indices for wild boar

Daishi Higashide, Takeo Kuriyama, Shun Takagi, Yoshihiro Nakashima, Keita Fukasawa, Gota Yajima, Minoru Kasada & Mayumi Yokoyama
Population growth in wild boars and feral pigs (Sus scrofa) has negative environmental and economic implications worldwide. Accordingly, it is necessary to monitor population trends for appropriate management. Despite the potential for bias, relative abundance indices based on signs of activity have the potential to be practical, low-cost monitoring tools for data collection at a local scale and over large areas. However, few studies have examined the effectiveness of specific signs as measures of relative...

Datasets for phylogenetic analyses of Pavlomulina ranunculiformis

Ryoma Kamikawa, Masanobu Kawachi, Takuro Nakayama, Motoki Kayama, Mami Nomura, Hideaki Miyashita, Othman Bojo, Lesley Rhodes, Stuart Sym, Richard Pienaar, Ian Probert & Isao Inouye
Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton, which is responsible for around 50% of global net primary production. However, the phenotypic identity of many of the organisms distinguished by environmental DNA sequences remains unclear. The rappemonads are a plastid-bearing protistan lineage that to date has only been identified by environmental plastid 16S rRNA sequences. The phenotypic identity of this group, which does not...

Temporal and interspecific dietary variation in wintering ducks in agricultural landscapes

Haruko Ando, Susumu Ikeno, Ayu Narita, Taketo Komura, Atsushi Takada, Yuji Isagi, Tomomi Inoue & Akio Takenaka
Farmlands are becoming more important as waterfowl foraging habitats, while natural wetlands are being lost globally. However, it is unclear how waterfowl coexist in agricultural landscapes by resource partitioning. We evaluated the diets of seven sympatric dabbling ducks foraging in rice paddy and lotus fields around Lake Kasumigaura, the second largest lake in Japan, during two wintering seasons (from November to February) by fecal DNA metabarcoding using chloroplast trnL and mitochondrial CO1 region sequences. We...

Has long-distance flight ability been maintained by pigeons in highly insular habitats?

Daichi Tsujimoto, Haruko Ando, Hajime Suzuki, Kazuo Horikoshi, Nobuyoshi Nakajima, Yoshihisa Suyama, Ayumi Matsuo, Chieko Fujii & Yuji Isagi
Aim: A reduction in dispersal ability has been thought to be a general trend for island land birds because of their physical isolation to a limited area, scarcity of predators, and ability to forage without flight in island habitats. However, recent studies have indicated that long-distance dispersal among island habitats may be maintained in island pigeon populations, which may be related to unstable food resource availability on a single island. Here, we investigated whether pigeons...

Areal (+)-borneol modulates root morphology, auxin signalling and meristematic activity in Arabidopsis roots

Junji Takabayashi, Kyohei Fukuda, Masayoshi Uefune, Hidehiro Fukaki, Yasuo Yamauchi, Ikuko Hara-Nishimura, Rika Ozawa, Kenji Matsui, Kazunori Okada, Ryozo Imai, Kenshi Takahashi, Shinichi Enami, Rene Wurst & Junji Takabayashi
One of the characteristic aspects of odour sensing in humans is the activation of olfactory receptors in a slightly different manner to different enantiomers. Here, we focused on whether plants showed enantiomer-specific responses similar to that in humans. We exposed Arabidopsis seedlings to methanol (control) and (+)- or (−)-borneol, and found that only (+)-borneol reduced the root length. Furthermore, the root-tip width was more increased upon (+)-borneol exposure than upon (−)-borneol exposure. In addition, root-hair...

Data from: Global stability of obligate mutualistm in community modules with facultative mutualists

Gaku Takimoto & Kenta Suzuki
Mutualism is a fundamental building block of ecological communities and an important driver of biotic evolution. Classic theory suggests that a pairwise two-species obligate mutualism is fragile, with a large perturbation potentially driving both mutualist populations into extinction. In nature, however, there are many cases of pairwise obligate mutualism. Such pairwise obligate mutualisms are occasionally associated with additional interactions with facultative mutualists. Here, we use a mathematical model to show that when a two-species obligate...

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: 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: 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: 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...

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...

The percentage of total agricultural area under maize, rice, wheat, vegetables, pulses and fruit production, by country, subject to water scarcity in 2050 as estimated from a multi-model ensemble

N. Fitton, P. Alexander, N. Arnell, B. Bajzelj, K. Calvin, J. Doelman, J.S. Gerber, P. Havlik, T. Hasegawa, M. Herrero, T. Krisztin, H. Van Meijl, T. Powell, R. Sands, E. Stehfest, P.C. West & P. Smith
Projections of global changes in water scarcity with the current extent of maize, rice, wheat, vegetables, pulses and fruit production commodities were combined to identify the potential country level vulnerabilities of cropland land to water scarcity in 2050. The data relate to an analysis of the impact changes in water availability will have on maize, rice, wheat, vegetables, pulses and fruit production commodities availability in 2050.

Data from: Climate and local environment structure asynchrony and the stability of primary production in grasslands

Benjamin Gilbert, Andrew MacDougall, Taku Kadoya, Munemitsu Akasaka, Joseph Bennett, Eric Lind, Habacuc Flores-Moreno, Jennifer Firn, Yann Hautier, Elizabeth Borer, Eric Seabloom, Peter Adler, Elsa Cleland, James Grace, W. Harpole, Ellen Esch, Joslin Moore, Jean Knops, Rebecca McCulley, B. Mortensen, J. Bakker & Philip Fay
Aim: Climate variability threatens to destabilize production in many ecosystems. Asynchronous species dynamics may buffer against such variability when decreased performance by some species is offset by increased performance of others. However, high climatic variability can eliminate species through stochastic extinctions or cause similar stress responses among species, reducing buffering. Local conditions, such as soil nutrients, can further alter production stability directly or by influencing asynchrony. We test these hypotheses using a globally distributed sampling...

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: Differential population responses of native and alien rodents to an invasive predator, habitat alteration, and plant masting

Keita Fukasawa, Tadashi Miyashita, Takuma Hashimoto, Masaya Tatara & Shintaro Abe
Invasive species and anthropogenic habitat alteration are major drivers of biodiversity loss. When multiple invasive species occupy different trophic levels, removing an invasive predator might cause unexpected outcomes due to complex interactions among native and non-native prey. Moreover, external factors such as habitat alteration and resource availability can affect such dynamics. We hypothesized that native and non-native prey respond differently to an invasive predator, habitat alteration, and bottom–up effects. To test the hypothesis, we used...

Data from: Evaluating the existence and benefit of major histocompatibility complex-based mate choice in an isolated owl population

Akira Sawada, Haruko Ando & Masaoki Takagi
How mate preferences evolve in the first place has been a major conundrum for sexual selection. Some hypotheses explaining this assume fitness benefit derived from subsequent generations. Major Histocompatibility Complex (MHC)-based mate choice is a representative example of the mate choice that is associated with such trans-generational mechanisms. To provide evidences for fitness benefit of MHC-based mate choice, previous studies assessed the association between own MHC genotype and own fitness components. However, the association between...

Data from: Evaluation of plant contamination in metabarcoding diet analysis of a herbivore

Haruko Ando, Chieko Fujii, Masataka Kawanabe, Yoshimi Ao, Tomomi Inoue & Akio Takenaka
Fecal DNA metabarcoding is currently used in various fields of ecology to determine animal diets. Contamination of non-food DNA from complex field environments is a considerable challenge to the reliability of this method but has rarely been quantified. We evaluated plant DNA contamination by sequencing the chloroplast trnL P6 loop region from food-controlled geese feces. The average percentage of contaminant sequences per sample was 1.86%. According to the results of generalized linear models, the probability...

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