129 Works

Data from: Evolutionary and dispersal history of Eurasian wild mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA

Hitoshi Suzuki, Mitsuo Nunome, Ghota Kinotshita, K. P. Aplin, Peter Vogel, Alexey P. Kryukov, Mei-Lei Jin, Sang-Hoon Han, Ibnu Maryanto, Kimiyuki Tsuchiya, Hidetoshi Ikeda, T. Shiroishi, Hiromichi Yonekawa & Kazuo Moriwaki
We examined sequence variation of mitochondrial DNA control region and cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from ca. 200 localities, with 290 new samples drawn primarily from previously unsampled portions of their Eurasian distribution and with the objective of further clarifying evolutionary episodes of this species before and after the onset of human-mediated long-distance dispersals. Phylogenetic analysis of the expanded data detected five equally distinct clades, with geographic ranges...

Data from: Effects of spatial structure of population size on the population dynamics of barnacles across their elevational range

Keiichi Fukaya, Takehiro Okuda, Masahiro Nakaoka & Takashi Noda
1. Explanations for why population dynamics vary across the range of a species reflect two contrasting hypotheses: (1) temporal variability of populations is larger in the centre of the range compared to the margins because overcompensatory density dependence destabilizes population dynamics, and (2) population variability is larger near the margins, where populations are more susceptible to environmental fluctuations. In both of these hypotheses, positions within the range are assumed to affect population variability. 2. In...

Data from: Effects of aphid parasitism on host plant fitness in an aphid-host relationship.

Saori Watanabe, Yuuka Murakami & Eisuke Hasegawa
Aphids are serious agricultural insect pests which exploit the phloem sap of host plants and thus transmit pathogens to their hosts. However, the degree to which aphid parsitism affects the fitness of the host plants is not well understood. The aphid, Macrosiphoniella yomogicola, parasitizes the mugwort Artemisia montana in Japan. During summer most mugworts carry aphids, but most aphid colonies die out after the budding of A. montana inflorescences in late summer. A few aphid...

Data from: Variations in ramet performance and the dynamics of an alpine evergreen herb, Gentiana nipponica, in different snowmelt conditions

Yuka Kawai & Gaku Kudo
Premise of the study: Variation in demographic parameters reflects the life-history strategies of plants in response to specific environments. We aimed to investigate the intraspecific variation in life-history traits of a clonal alpine herb, Gentiana nipponica, in various snowmelt conditions. Methods: Individual ramets within genets accumulate leaves for 7-9 years without shedding, and die after reproduction. We tested the physiological function of accumulated leaves for reproduction and monitored the ramet demography in early, intermediate, and...

Correlation of giant earthquakes with the lunar phase in seven Indo-Pacific subduction zones and around Mongolia

Yoshiaki Fujii, Yusuke Tsuboi, Anjula Dassanayake, Junichi Kodama, Daisuke Fukuda & Badrul Alam
Lunar phases of earthquakes worldwide with MW ≥ 8 between 1900 and November 15, 2016, were calculated. The null hypothesis that the occurrences of the giant earthquakes are random was assumed and tested for some subduction zones and around Mongolia. The null hypothesis was statistically rejected for Southern Chile, Alaska, Peru, the Japan Trench, the Kuril Islands, and Around Mongolia. The rejection of the random null hypothesis means that the occurrences of the giant earthquakes...

Dataset for group living and duetting in barbet species

Masayo Soma & Henrik Brumm
The duets of birds have intrigued biologists for a long time, yet much remains unknown about the evolution of these striking collective displays. This is because previous studies on duet evolution have been biased to songbirds and neglected other bird groups. In songbirds, the absence of migration has been found to predict the occurrence of duetting, indirectly supporting the idea that duet communication is linked with pair-bonding. Here, we used phylogenetic comparative analyses in a...

Insights from Fisher's geometric model on the likelihood of speciation under different histories of environmental change

Ryo Yamaguchi & Sarah P. Otto
All code and simulation data necessary to repeat the analysis described in "Insights from Fisher’s geometric model on the likelihood of speciation under different histories of environmental change."

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: 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...

Influence of Quaternary environmental changes on mole populations inferred from mitochondrial sequences and evolutionary rate estimation

Hitoshi Suzuki, Azusa Nakamoto, Masashi Harada, Reiko Mitsuhashi, Kimiyuki Tsuchiya, Alexey P. Kryukov & Akio Shinohara
Quaternary environmental changes fundamentally influenced genetic diversity of the temperate-zone terrestrial animals, including those on the Japanese Archipelago. The genetic diversity of present-day populations are taxon and region specific, but its determinants are poorly understood. Here, we analyzed cytochrome b gene (Cytb) sequences (1,140 bp) of mitochondrial DNA (mtDNA) to elucidate factors determining the genetic variation in three species of large moles: Mogera imaizumii and Mogera wogura occur in Northern and Southern mainland Japan (Honshu,...

Data from: Deep phylogeographic structure and parallel host range evolution in the leaf beetle Agelasa nigriceps

Tetsuo I. Kohyama, Kazuma Matsumoto & Haruo Katakura
To understand the mechanisms behind the diversification of herbivorous insects through insect-plant interactions, it is important to know how the insects change their diet breadth in response to environmental changes. In this study, we investigated the phylogeographic pattern of the leaf beetle Agelasa nigriceps to infer the evolutionary history of its host range. While this beetle commonly uses Actinidia arguta (Actinidiaceae) as a host plant, it has been recorded recently on Pterostyrax hispidus (Styracaceae), which...

Data from: How many broadleaved trees are enough in conifer plantations? The economy of land sharing, land sparing, and quantitative targets

Yuichi Yamaura, Yasushi Shoji, Yasushi Mitsuda, Hajime Utsugi, Takahiro Tsuge, Koichi Kuriyama & Futoshi Nakamura
1. For biodiversity conservation to be an effective and significant social investment, non-marketed values of biodiversity conservation and its associated opportunity costs should be evaluated in monetary terms. 2. In this study, we measured the willingness to pay (WTP) for bird abundance using a choice experiment (CE) based on the random utility model. We performed a cost–benefit analysis to identify the optimal proportion of broad-leaved trees in conifer plantations on a volume basis to maximize...

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: 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: Definition and estimation of vital rates from repeated censuses: choices, comparisons and bias corrections focusing on trees

Takashi S. Kohyama, Tetsuo I. Kohyama, Douglas Sheil & Takashi Kohyama
1.Mortality and recruitment rates are fundamental measures of population dynamics. Ecologists and others have defined and estimated these vital rates in various ways. We review these alternatives focusing on tree population census data in fixed area plots, though many aspects have wider application when similar data characteristics and assumptions apply: our goal is to guide choices and facilitate comparisons. 2.We divide our estimates into ‘instantaneous’ and ‘annual’ rates, corresponding to continuous- or discrete-time dynamics respectively....

Data from: Eversion and withdrawal of an intromittent organ before sexual maturation prepares male beetles for copulation

Yoko Matsumura & Takuya Kubo
Some species of criocerine beetles have a hyper-elongated part of the intromittent organ called a flagellum. In resting position, the flagellum is stored in a specialized internal sac in the intromittent organ. This specialized state of the flagellum and internal sac is indispensable during copulation for flagellar insertion into the female spermathecal duct for sperm transfer. However, the morphogenesis of the flagellum does not generate the active state of the flagellum; rather, the flagellum is...

Insecticide resistance governed by gut symbiosis in a rice pest, Cletus punctiger, under laboratory conditions

Kota ISHIGAMI, Seonghan JANG, Hideomi ITOH & Yoshitomo KIKUCHI
Resistance to toxins in insects is generally thought of as their own genetic trait, but recent studies have revealed that gut microorganisms could mediate resistance by detoxifying phytotoxins and man-made insecticides. By laboratory experiments, we here discovered a striking example of gut symbiont-mediated insecticide resistance in a serious rice pest, Cletus punctiger. The rice bug horizontally acquired fenitrothion-degrading Burkholderia through oral infection and housed it in midgut crypts. Fenitrothion-degradation test revealed that the gut-colonizing Burkholderia...

Data from: Widespread grounding line retreat of Totten Glacier, East Antarctica, over the 21st century

Tyler Pelle, Mathieu Morlighem, Helene Seroussi & Yoshihiro Nakayama
Totten Glacier, the primary ice discharger of East Antarctica, contains 3.85 m sea level rise equivalent ice mass (SLRe) and has displayed ocean-driven dynamic change since at least the early 2000s. We project Totten’s evolution through 2100 in a fully coupled ice-ocean model, forced at the ocean boundaries with anomalies in CMIP6 projected temperature, salinity, and velocity. Consistent with previous studies, the Antarctic Slope Current continues to modulate warm water inflow towards Totten in future...

Data from: Early origin of sweet perception in the songbird radiation

Yasuka Toda, Meng-Ching Ko, Qiaoyi Liang, Eliot Miller, Alejandro Rico-Guevara, Tomoya Nakagita, Ayano Sakakibara, Kana Uemura, Timothy Sackton, Takashi Hayakawa, Simon Yung Wa Sin, Yoshiro Ishimaru, Takumi Misaka, Pablo Oteiza, James Crall, Scott Edwards, Shuichi Matsumura & Maude Baldwin
Early events in the evolutionary history of a clade can shape the sensory systems of descendant lineages. Although the avian ancestor may not have had a sweet receptor, the widespread incidence of nectar-feeding birds suggests multiple acquisitions of sugar detection. In this study, we identify a single early sensory shift of the umami receptor (the T1R1-T1R3 heterodimer) that conferred sweet-sensing abilities in songbirds, a large radiation containing nearly half of all living birds. We demonstrate...

Data from: Contribution of small isolated habitats in creating refuges from biological invasions along a geomorphological gradient of floodplain waterbodies

Nobuo Ishiyama, Kazuki Miura, Satoshi Yamanaka, Junjiro Negishi & Futoshi Nakamura
1. Habitat fragmentation, which involves habitat size reduction and isolation, is a major cause of biodiversity decline. However, interest in small isolated habitats has increased among ecosystem managers because these fragments can serve as remnant refuges for unique and/or endangered species in human-altered landscapes. 2. In a fragmented floodplain of northern Japan, we demonstrate how habitat fragmentation and habitat quality shape the refuges for a unique endangered minnow (Rhynchocypris percnurus sachalinensis) from biological invasions. We...

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 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: Individual differences are consistent across changes in mating status and mediated by biogenic amines

Nicholas DiRienzo & Hitoshi Aonuma
Although aspects of an individual’s state are well-known to influence the expression of behavior, it is still unclear how elements of state affect consistent among-individual differences in behavior. With binary, irreversible elements of state, such as mating status, there may be optimal behavioral phenotypes before and after mating, with individuals often prioritizing mate acquisition before and resource acquisition after. Yet, limited plasticity may prevent optimal behavior in both contexts. Additionally, it remains largely unknown if...

Data from: Form–function relationships in a marine foundation species depend on scale: a shoot to global perspective from a distributed ecological experiment

Jennifer L. Ruesink, John J. Stachowicz, Pamela L. Reynolds, Christoffer Boström, Mathieu Cusson, James Douglass, Johan Eklöf, Aschwin H. Engelen, Masakazu Hori, Kevin Hovel, Katrin Iken, Per-Olav Moksnes, Masahiro Nakaoka, Mary I. O'Connor, Jeanine L. Olsen, Erik E. Sotka, Matthew A. Whalen & Emmett J. Duffy
Form-function relationships in plants underlie their ecosystem roles in supporting higher trophic levels through primary production, detrital pathways, and habitat provision. For widespread, phenotypically-variable plants, productivity may differ not only across abiotic conditions, but also from distinct morphological or demographic traits. A single foundation species, eelgrass (Zostera marina), typically dominates north temperate seagrass meadows, which we studied across 14 sites spanning 32-61° N latitude and two ocean basins. Body size varied by nearly two orders...

Data from: Winter warming effects on tundra shrub performance are species-specific and dependent on spring conditions

Eveline J. Krab, Jonas Rönnefarth, Marina Becher, Gesche Blume-Werry, Frida Keuper, Jonatan Klaminder, Juergen Kreyling, Kobayashi Makoto, Ann Milbau, Ellen Dorrepaal & Jonas Roennefarth
1. Climate change driven increases in winter temperatures positively affect conditions for shrub growth in arctic tundra by decreasing plant frost damage and stimulation of nutrient availability. However, the extent to which shrubs may benefit from these conditions may be strongly dependent on the following spring climate. Species-specific differences in phenology and spring frost sensitivity likely affect shrub growth responses to warming. Additionally, effects of changes in winter and spring climate may differ over small...

Registration Year

  • 2021
  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013
  • 2012

Resource Types

  • Dataset


  • Hokkaido University
  • Kyoto University
  • University of Tokyo
  • Forestry and Forest Products Research Institute
  • National Institute for Environmental Studies
  • Ryukoku University
  • University of British Columbia
  • Max Planck Institute for Ornithology
  • Tokyo Institute of Technology
  • University of Minnesota