16 Works

Data from: Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio

Toshifumi Minamoto, Kimiko Uchii, Teruhiko Takahara, Takumi Kitayoshi, Tsuji Satsuki, Hiroki Yamanaka, Hideyuki Doi & Satsuki Tsuji
The recently developed environmental DNA (eDNA) analysis has been used to estimate the distribution of aquatic vertebrates by using mitochondrial DNA (mtDNA) as a genetic marker. However, mtDNA markers have certain drawbacks such as variable copy number and maternal inheritance. In this study, we investigated the potential of using nuclear DNA (ncDNA) as a more reliable genetic marker for eDNA analysis by using common carp (Cyprinus carpio). We measured the copy numbers of cytochrome b...

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...

Data from: Biodiversity-ecosystem functioning relationships in long-term time series and palaeoecological records: deep sea as a test bed

Moriaki Yasuhara, Hideyuki Doi, Chih-Lin Wei, Roberto Danovaro & Sarah E. Myhre
The link between biodiversity and ecosystem functioning (BEF) over long temporal scales is poorly understood. Here, we investigate biological monitoring and palaeoecological records on decadal, centennial and millennial time scales from a BEF framework, by using deep-sea, soft-sediment environments as a test bed. Results generally show positive BEF relationships, in agreement with BEF studies based on present-day spatial analyses and short-term manipulative experiments. However, the deep-sea BEF relationship is much noisier across longer time scales...

Data from: Distribution and drift dispersal dynamics of a caddisfly grazer in response to resource abundance and its ontogeny

Izumi Katano, Hiromune Mitsuhashi, Hideyuki Doi, Yu Isobe & Tadashi Oishi
Stream grazers have a major impact on food web structure and the productivity of stream ecosystems; however, studies on the longitudinal (upstream versus downstream) and temporal changes in their drift dynamics and resulting distributions remain limited. Here, we investigated the longitudinal and temporal distributions and drift propensity of a trichopteran grazer, the caddisfly, Micrasema quadriloba, during its life cycle in a Japanese stream. The distribution of larvae significantly shifted downstream during the fifth instar larval...

Data from: Starvation effects on nitrogen and carbon stable isotopes of animals: an insight from meta-analysis of fasting experiments

Hideyuki Doi, Fumikazu Akamatsu & Angélica L. González
Nitrogen and carbon stable isotopic compositions (δ15N and δ13C) of consumers have been used for physiological and food web studies. Previous studies have shown δ15N and δ13C values are affected by several biological and environmental factors during starvation, but the generality of the effect of starvation on δ15N and δ13C values has not yet been tested. Here, we performed a meta-analysis to evaluate the effects of starvation on δ15N and δ13C values of consumers, and...

Data from: Trophic niche breadth of pond zooplankton species using stable isotope analysis and the relationship with the abiotic and biotic factors

Hideyuki Doi, Kwang-Hyeon Chang & Shin-Ichi Nakano
1. Zooplankton species have different feeding habits, but the diversity of their food resources and the factors governing them are still largely unknown. We here estimated the differences in the trophic niche breadths of dominant zooplankton species in ponds, using stable isotopes. 2. To understand the differences in trophic niches of different zooplankton species, we measured the carbon and nitrogen stable isotope ratios and calculated the nearest neighbor distance (NND), and standard deviation of NND...

Data from: Critically endangered island endemic or peripheral population of a widespread species? Conservation genetics of Kikuchi’s gecko and the global challenge of protecting peripheral oceanic island endemic vertebrates

Cameron D. Siler, Jamie R. Oaks, Kerry Cobb, Hidetoshi Ota & Rafe M. Brown
Aim: To highlight the significant conservation challenge of evaluating peripheral endemic vertebrates in island archipelago systems and to assess empirically the complexities of approaches to conservation genetic studies across political and biogeographic boundaries. To demonstrate the poignant need for international collaboration and coordination when species delimitation problems with high conservation concern involve island endemics with biogeographically peripheral ranges. Location: Southeast Asia, Lanyu Island, Taiwan, and the Philippines. Methods: Genetic samples were collected and sequenced for...

Data from: Ontogenetic trajectories of septal spacing in Early Jurassic belemnites from Germany and France, and their palaeobiological implications

Ryoji Wani, Amane Tajika, Kenji Ikuno & Tetsuro Iwasaki
Based on well-preserved belemnites, the ontogenetic trajectories of septal spacing between succeeding chambers were analysed. In the examined species (Passaloteuthis laevigata, Parapassaloteuthis zieteni and Pseudohasitites longiformis) that come from Buttenheim, Germany, and Lixhausen, France, the ontogenetic trajectories of septal spacing follow exponentially increasing trends with no decreasing phase of septal crowding during the earliest ontogenetic stage. The absence of a decreasing trend at the earliest ontogenetic stage is a unique character in contrast with those...

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...

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...

Effects of temperature on seed dormancy and germination of the coastal dune plant Viola grayi: Germination phenology and responses to winter warming

Asumo Kuroda & Yoshihiro Sawada
PREMISE: In temperate sand dunes, rising air temperature owing to climate change could not only further elevate surface soil temperatures during summers but also drastically change the range of soil temperatures in other seasons. Winter warming may shift the timing of seed germination of dune species that require cold stratification for dormancy release. METHODS: We assessed the effects of temperature on dormancy and germination of Viola grayi seeds and evaluated whether winter warming could affect...

Data from: Detection of an endangered aquatic heteropteran using environmental DNA in a wetland ecosystem

Hideyuki Doi, Izumi Katano, Yusuke Sakata, Rio Souma, Toshihiro Kosuge, Mariko Nagano, Kousuke Ikeda, Koki Yano & Koji Tojo
The use of environmental DNA (eDNA) has recently been employed to evaluate the distribution of various aquatic macroorganisms. Although this technique has been applied to a broad range of taxa, from vertebrates to invertebrates, its application is limited for aquatic insects such as aquatic heteropterans. Nepa hoffmanni (Heteroptera: Nepidae) is a small (approx. 23 mm) aquatic heteropteran that inhabits wetlands, can be difficult to capture and is endangered in Japan. The molecular tool eDNA was...

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: Prolonged impacts of past agriculture and ungulate overabundance on soil fungal communities in restored forests

Shinichi Tatsumi, Shunsuke Matsuoka, Saori Fujii, Kobayashi Makoto, Takashi Osono, Forest Isbell & Akira Mori
Soil fungi can help improve ecosystem restoration, yet our understanding of how they reassemble in degraded land is limited. Here, using DNA metabarcoding, we studied the fungal community structure in reforested sites following agricultural abandonment and ungulate overabundance. Two treatments, namely ‘reforestation using different numbers of tree species’ and ‘deer exclusion,’ have been applied for multiple decades in the study sites. We found that local fungal richness (alpha diversity) and total fungal richness (gamma diversity)...

Museomics contributes to the spatiotemporal assessment of genetic diversity and structure in wild and ex situ conservation organisms: a case study of three endangered coastal plants in Japan

Naoyuki Nakahama, Shuji Matsumoto, Takeshi Asai, Atsuko Takano, Nana Morita, Ayumi Matsuo, Yoshihisa Suyama & Asumo Kuroda
Understanding the extent to which genetic diversity of wild populations in ex situ conservation can be retained is crucial for the management of such populations. Wild individuals collected in the target area in the past and present can be used to estimate the number of alleles lost over time in wild populations and thereby the number of alleles whose loss could be prevented by ex situ conservation. Here, we assessed the genetic diversity of wild...

Data from: Terrigenous subsidies in lakes support zooplankton production mainly via a green food chain and not the brown food chain

Jotaro Urabe, Fumiya Hirama, Hideyuki Doi, Takehiro Kazama, Takumi Noguchi, Tyler H. Tappenbeck, Izumi Katano, Masato Yamamichi, Takehito Yoshida & James J. Elser
Terrestrial organic matter (t-OM) has been recognized as an important cross-boundary subsidy to aquatic ecosystems. However, recent evidence has shown that t-OM contributes little to promote secondary production in lakes because it is low quality food for aquatic consumers. To resolve this conflict, we performed a field experiment using leaf litter as t-OM. In the experiment, we monitored zooplankton biomass in enclosures with and without addition of leaf litter under shaded and unshaded conditions and...

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