16 Works

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: Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary Ice Age events with inferred population expansions and dispersals in Japanese Apodemus

Yutaro Suzuki, Tomozawa Morihiko, Yuki Koizumi, Kimiyuki Tsuchiya & Hitoshi Suzuki
Background: Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely...

Data from: Life-history characteristics and landscape attributes as drivers of genetic variation, gene flow and fine-scale population structure in Northern Dolly Varden (Salvelinus malma malma) in Canada

Les N. Harris, Robert Bajno, Colin P. Gallagher, Itsuro Koizumi, Lucy K. Johnson, Kimberly L. Howland, Eric B. Taylor & James D. Reist
The Northern Dolly Varden (Salvelinus malma malma) displays variable life-history types and occupies freshwater habitats with varying levels of connectivity. Here, we assayed microsatellite DNA variation in Northern Dolly Varden from the western Canadian Arctic to resolve landscape and life history variables driving variation in genetic diversity and population structure. Overall, genetic variation was highest in anadromous populations and lowest in those isolated above waterfalls with stream-resident forms intermediate between the two. Anadromous and isolated...

Data from: The distribution of cool spots as microrefugia in a mountainous area

Ayuma Shimokawabe, Yuichi Yamaura, Takumi Akasaka, Tomonori Sato, Yuichiro Shida, Satoshi Yamanaka & Futoshi Nakamura
It has recently been proposed that microrefugia played an important role in species survival during past climate change events. However, the current distributions of microrefugia remain largely unknown. Wind-hole sites are areas affected by preferential flows of cool air generated in interstitial spaces created by rock fragments or colluvia. Alpine plant species occurring in lowland wind-hole sites isolated from alpine zones may be relicts of the last glacial period. Hokkaido, northern Japan, is known to...

Data from: Hypoperfusion of the adventitial vasa vasorum develops an abdominal aortic aneurysm

Hiroki Tanaka, Nobuhiro Zaima, Takeshi Sasaki, Masaki Sano, Naoto Yamamoto, Takaaki Saito, Kazunori Inuzuka, Takahiro Hayasaka, Naoko Goto-Inoue, Yuki Sugiura, Kohji Sato, Hirona Kugo, Tatsuya Moriyama, Hiroyuki Konno, Mitsutoshi Setou & Naoki Unno
The aortic wall is perfused by the adventitial vasa vasorum (VV). Tissue hypoxia has previously been observed as a manifestation of enlarged abdominal aortic aneurysms (AAAs). We sought to determine whether hypoperfusion of the adventitial VV could develop AAAs. We created a novel animal model of adventitial VV hypoperfusion with a combination of a polyurethane catheter insertion and a suture ligation of the infrarenal abdominal aorta in rats. VV hypoperfusion caused tissue hypoxia and developed...

Data from: The influence of preceding dive cycles on the foraging decisions of Antarctic fur seals

Takashi Iwata, Kentaro Q. Sakamoto, Ewan W. J. Edwards, Ian J. Staniland, Philip N. Trathan, Yusuke Goto, Katsufumi Sato, Yasuhiko Naito & Akinori Takahashi
The foraging strategy of many animals is thought to be determined by their past experiences. However, few empirical studies have investigated whether this is true in diving animals. We recorded three-dimensional movements and mouth-opening events from three Antarctic fur seals during their foraging trips to examine how they adapt their behaviour based on past experience—continuing to search for prey in the same area or moving to search in a different place. Each dive cycle was...

Data from: Transcriptome analysis of predator- and prey-induced phenotypic plasticity in the Hokkaido salamander (Hynobius retardatus)

Masatoshi Matsunami, Jun Kitano, Osamu Kishida, Hirofumi Michimae, Toru Miura & Kinya Nishimura
Predator- and prey-induced phenotypic plasticity is widely observed among amphibian species. Although ecological factors inducing diverse phenotypic responses have been extensively characterized, we know little about the molecular bases of variation in phenotypic plasticity. Larvae of the Hokkaido salamander, Hynobius retardatus, exhibit two distinct morphs: the presence of their prey, Rana pirica tadpoles, induces a broad-headed attack morph, and the presence of predatory dragonfly nymphs (Aeshna nigroflava) induces a defence morph with enlarged external gills...

Data from: Ancient onset of geographic divergence, interpopulation genetic exchange, and natural selection on the Mc1r coat-color gene in the house mouse (Mus musculus) inferred from tandemly arranged nuclear gene markers

Sayaka Kodama, Mitsuo Nunome, Hitoshi Suzuki & Kazuo Moriwaki
We examined genetic variation in house mice from India and Pakistan, a predominant part of the predicted homeland of this species and also the territory of the subspecies Mus musculus castaneus (CAS), using a nuclear marker for seven tandemly arranged genes (Fanca–Spire2–Tcf25–Mc1r–Def8–Afg3l1–Dbndd1) and compared them with those previously determined for mice from other parts of Eurasia. Construction of a network with the concatenate sequences yielded three distinct clusters representing the three major subspecies groups: CAS,...

Data from: Does nest predation risk affect the frequency of extra-pair paternity in a socially monogamous passerine?

Teru Yuta & Itsuro Koizumi
While considerable variations in both the frequency of extra-pair paternity (EPP) and the behavioral events that produce it are recognized among species, populations, individuals, and breeding attempts, the determinants of these variations are surprisingly difficult to establish. Nest predation may be one such determinant, since it is the most important source of reproductive failure, and past studies have suggested a variety of reproductive flexibilities under nest predation risk. However, despite its potentially significant effect on...

Data from: Feather corticosterone reveals stress associated with dietary changes in a breeding seabird

Alexis P. Will, Yutaka Watanuki, Dale M. Kikuchi, Nobuhiko Sato, Motohiro Ito, Matt Callahan, Katherine Wynne-Edwards, Scott Hatch, Kyle H. Elliott, Leslie Slater, Akinori Takahashi, Alexander S. Kitaysky, Kyle Elliott, Alexis Will & Alexander Kitaysky
Changes in climate and anthropogenic pressures might affect the composition and abundance of forage fish in the world's oceans. The junk-food hypothesis posits that dietary shifts that affect the quality (e.g., energy content) of food available to marine predators may impact their physiological state and consequently affect their fitness. Previously, we experimentally validated that deposition of the adrenocortical hormone, corticosterone, in feathers is a sensitive measure of nutritional stress in seabirds. Here, we use this...

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: Feeding evolution of a herbivore influences an arthropod community through plants: implications for plant-mediated eco-evolutionary feedback loop

Shunsuke Utsumi
1. Genetic variation in individual species can have important ecological consequences, and sometimes, these interactions are mediated through another species. For example, genetic variation in an herbivore could alter plant responses that then influence other plant-associated arthropods. However, few systems have experimentally tested the ecological consequences of genetic variation as mediated through other species, especially within the same trophic community context. 2. I studied how evolution of feeding preference in the willow leaf beetle (Plagiodera...

Data from: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

Masaki Miya, Yukuto Sato, Tsukasa Fukunaga, Tetsuya Sado, Jan Y. Poulsen, Keiichi Sato, Toshifumi Minamoto, Satoshi Yamamoto, Hiroki Yamanaka, Hitoshi Araki, Michio Kondoh & Wataru Iwasaki
We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163–185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility...

Data from: A FISH-based chromosome map for the European corn borer yields insights into ancient chromosomal fusions in the silkworm

Yuji Yasukochi, Mizuki Ohno, Fukashi Shibata, Akiya Jouraku, Ryo Nakano, Yukio Ishikawa & Ken Sahara
A significant feature of the genomes of Lepidoptera, butterflies and moths, is the high conservation of chromosome organization. Recent remarkable progress in genome sequencing of Lepidoptera has revealed that syntenic gene order is extensively conserved across phylogenetically distant species. The ancestral karyotype of Lepidoptera is thought to be n = 31; however, that of the most well studied moth, Bombyx mori, is n = 28, and diverse studies suggest that three chromosomal fusion events occurred...

Data from: Insecticide applications to soil contribute to development of Burkholderia mediating insecticide resistance in stinkbugs

Kanako Tago, Yoshitomo Kikuchi, Shinji Nakaoka, Chie Katsuyama, Masahito Hayatsu & Sinji Nakaoka
Some soil Burkholderia strains are capable of degrading the organophosphorus insecticide, fenitrothion, and establish symbiosis with stinkbugs, making the host insects fenitrothion-resistant. However, the ecology of the symbiotic degrading Burkholderia adapting to fenitrothion in the free-living environment is unknown. We hypothesized that fenitrothion applications affect the dynamics of fenitrothion-degrading Burkholderia, thereby controlling the transmission of symbiotic degrading Burkholderia from the soil to stinkbugs. We investigated changes in the density and diversity of culturable Burkholderia (i.e....

Data from: Size of dominant diatom species can alter their evenness

Koji Sugie & Koji Suzuki
Traditionally, biodiversity has often been estimated on the basis of abundance partly due to the need for complicated measurements of biomass. Here, we conducted robust measurements of the community composition and of the size structure of diatoms in the North Pacific to evaluate the importance of biomass on the biodiversity. We found that the two most useful evenness indices increased in most cases where small species were numerically dominant when calculations were based on biomass...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Hokkaido University
  • University of Tokyo
  • Kanagawa Prefectural Museum of Natural History
  • National Institute for Environmental Studies
  • Keio University
  • National Institute of Polar Research
  • Kitasato University
  • Tokyo Metropolitan University
  • Ryukoku University