119 Works

Role of ancient lakes in genetic and phenotypic diversification of freshwater snails

Takahiro Hirano, Takumi Saito, Yoshihiro Tsunamoto, Joichiro Koseki, Larisa Prozorova, Do Tu, Keiji Matsuoka, Katsuki Nakai, Yoshihisa Suyama & Satoshi Chiba
Endemic organisms of ancient lakes have been studied as models to understand processes of speciation and adaptive radiation. However, it remains unclear how ancient lakes play roles in genetic and phenotypic diversity of freshwater mollusks. In the present study, we focus on viviparid freshwater snails in the ancient lakes of East and Southeast Asia (Japan and China) to address this question. Using molecular phylogenetic analyses based on mitochondrial (COI, 16S) and nuclear genes (18S, 28S,...

Disruptive selection of shell colour in land snails: a mark–recapture study of Euhadra peliomphala simodae

Shun Ito & Junji Konuma
Many theoretical studies have suggested that disruptive selection plays an important role in phenotypic divergence, but few studies have determined the action of disruptive selection on phenotypic divergence via field studies. This study investigated the effect of disruptive selection on shell colour polymorphism in the Japanese land snail Euhadra peliomphala simodae to determine whether extreme phenotypes of snail shell colour are favored over intermediate phenotypes. We conducted field surveys on an oceanic island with black,...

Seasonal change in male reproductive investment of a fish

Shingo Fujimoto, Mitsuharu Yagi, Kazunori Yamahira & Satoshi Takeda
Many animals are sexually dimorphic, whereby males may display brighter body coloration and more distinctive ornamentation than females. Fishes in temperate regions markedly change their energy allocation toward reproduction in response to the seasonal environment. Seasonal change in reproductive investment affects the expression of sexually dimorphic traits in males through gonadal weight change. Here, we report seasonal changes in body size, testis weight and sexual dimorphism of the fins (anal fin length and dorsal fin...

Dataset for: Image-based screen capturing misfolding status of Niemann-Pick type C1 identifies potential candidates for chaperone drugs

Kenji Ohgane, Ryuta Shioi, Fumika Karaki, Hiromasa Yoshioka, Tomomi Noguchi-Yachide, Minoru Ishikawa, Kosuke Dodo, Mikiko Sodeoka & Yuichi Hashimoto
Niemann-Pick disease type C is a rare, fatal neurodegenerative disorder characterized by massive intracellular accumulation of cholesterol. In most cases, loss-of-function mutations in NPC1 gene that encodes for a lysosomal cholesterol transporter NPC1 are responsible for the disease, and more than half of the mutations are considered to interfere with biogenesis or folding of the protein. Previously we have identified a series of oxysterol derivatives and phenanthridine-6-one derivatives as pharmacological chaperones, small molecules that rescue...

Data from: Climate-mediated changes in predator–prey interactions in the fossil record: a case study using shell-drilling gastropods from the Pleistocene Japan Sea

Tomoki Chiba & Shin'ichi Sato
Paleoecological studies enhance our understanding of biotic responses to climate change because they consider long timescales not accessible through observational and experimental studies. Using predatory drillholes produced on fossil bivalve shells by carnivorous gastropods, we provide an example of how climate change affected predator–prey interactions. We quantitatively examine temporal changes in fossil molluscan assemblages and predation patterns from the Pleistocene Japan Sea, which experienced drastic environmental changes in relation to glacial–interglacial climate cycles. We found...

Non-biodegradable objects may boost microbial growth in water bodies by harnessing bubbles

Atul Srivastava, Kenji Kikuchi & Takuji Ishikawa
Given the ubiquity of bubbles and non-biodegradable wastes in aqueous environments, their transport through bubbles should be widely extant in water bodies. In this study, we investigate the effect of bubble-induced waste transport on microbial growth by using yeasts as model microbes and a silicone rubber object as a model waste. Noteworthily, this object repeatedly rises and sinks in fluid through fluctuations in bubble acquired buoyant forces produced by cyclic nucleation, growth and release of...

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...

Verifiability of genus-level classification under quantification and parsimony theories: a case study of follicucullid radiolarians

Yifan Xiao, Noritoshi Suzuki, Weihong He, Michael Benton, Tinglu Yang & Chenyang Cai
The classical taxonomy of fossil invertebrates is based on subjective judgments of morphology, which can cause confusion since there are no codified standards for the classification of genera. Here, we explore the validity of the genus taxonomy of 75 species and morphospecies of the Follicucullidae, a Late Paleozoic family of radiolarians, using a new method, Hayashi’s quantification theory II (HQT-II), a general multivariate statistical method for categorical datasets relevant to discriminant analysis. We identify a...

Nonlinear time series analysis of the interaction between the citrus whitefly and the whitefly-specialist ladybird

Suzuki Noriyuki, Kazutaka Kawatsu & Shuji Kaneko
A comprehensive understanding of the top-down effects of natural enemies on agricultural pests is essential for achieving effective biological control in integrated pest management. However, it is typically difficult to identify causal effects between the interacting species from time series data, which have often been monitored for pest forecasting purposes in agricultural ecosystems, as it is likely to involve nonlinear (state-dependent) population dynamics. In this study, we applied a recently developed framework of nonlinear time...

Stable persistence of relict populations involved evolutionary shifts of reproductive characters in the genus Tanakaea (Saxifragaceae)

Daiki Takahashi
Tertiary relicts often show evolutionary stasis in morphology and ecology and have been hypothesised to retain stable population sizes in refugia. However, recent studies have reported that some relicts evolutionarily shifted their physiology, ecology, and morphology and experienced various patterns of demography. To understand the historical survival of relict plants, a multidimensional study investigating the evolution of ecological and morphological traits as well as population demographic history is needed. The genus Tanakaea (Saxifragaceae) comprises two...

Data from: Acoustic emissions of Sorex unguiculatus (Mammalia: Soricidae): assessing the echo-based orientation hypothesis

Lida Sanchez, Satoshi D. Ohdachi, Atsushi Kawahara, Lazaro M. Echenique-Diaz, Shinichiro Maruyama & Masakado Kawata
Shrew species have been proposed to utilize an echo-based orientation system to obtain additional acoustic information while surveying their environments. This system has been supported by changes in vocal emission rates when shrews encounter different habitats of varying complexity, although detailed acoustic features in this system have not been reported. In this study, behavioral experiments were conducted using the long-clawed shrew (Sorex unguiculatus) to assess this orientation system. Three experimental conditions were set, two of...

Data from: Anatomy and affinities of a new 535-million-year-old medusozoan from the Kuanchuanpu Formation, South China

Xing Wang, Jian Han, Jean Vannier, Qiang Ou, Xiaoguang Yang, Kentaro Uesugi, Osamu Sasaki & Tsuyoshi Komiya
We describe here Sinaster petalon gen. et sp. nov., a new embryonic form from the c. 535 million-year-old Kuanchuanpu Formation of South China (Ningqiang, Shaanxi Province). The excellent three-dimensional, phosphatic preservation of these microfossils allowed us to use x-ray microtomographic techniques to make accurate reconstructions of their internal structures and to compare their anatomy point-by-point with that of extant cnidarians and other animal groups. Sinaster petalon has anatomical features typical of extant Medusozoa (Cnidaria), such...

Data from: \"Development of the draft genome sequence of the marbled flounder Pseudopleuronectes yokohamae as a reference of population genomic analysis\" in Genomic Resources Notes accepted 1 February 2015 – 31 March 2015

Yuki Minegishi, Minoru Ikeda, Lynda F. Delph, Laura A. Weingartner, Peter D. Fields, Laura Bertini, Carla Caruso, Silvia Proietti, Wolfgang Arthofer, Francesco Cicconardi, Heike Ritthammer, Birgit C. Schlick-Steiner, Florian M. Steiner, Gregor A. Wachter & Herbert C. Wagner
This article documents the public availability of the draft genome sequence data (raw reads, assembled contigs and unassembled reads) and RAD-tag read data of the marbled flounder Pseudopleuronectes yokohamae (Pleuronectiformes; Pleuronectidae).

Data from: Long-term persisting hybrid swarm and geographic difference in hybridization pattern: genetic consequences of secondary contact between two Vincetoxicum species (Apocynaceae–Asclepiadoideae)

Yue Li, Fumito Tada, Tadashi Yamashiro & Masayuki Maki
Background: During glacial periods, glacial advances caused temperate plant extirpation or retreat into localized warmer areas, and subsequent postglacial glacial retreats resulted in range expansions, which facilitated secondary contact of previously allopatric isolated lineages. The evolutionary outcomes of secondary contact, including hybrid zones, dynamic hybrid swarm, and resultant hybrid speciation, depends on the strengths of reproductive barriers that have arisen through epistatic and pleiotropic effects during allopatric isolation. The aim of this study was to...

Data from: \"Transcriptome resources for two highly divergent Silene latifolia populations\" in Genomic Resources Notes accepted 1 February 2015 – 31 March 2015

Peter Fields, Laura Weingartner & Lynda Delph
Here we have used next-generation Illumina sequencing to generate transcriptomes of four S. latifolia individuals from two morphologically divergent populations from disparate habitats, including including two females from Xativa, Spain and two males from Zagreb, Croatia. Spanish plants experience a much hotter, drier climate than Croatian plants, and the populations have ecologically relevant differences in floral and leaf characteristics (e.g., Spain has thicker leaves and produces fewer, larger flowers in comparison) (data not shown). This...

Data from: Lack of genetic variation prevents adaptation at the geographic range margin in a damselfly

Yuma Takahashi, Yoshihisa Suyama, Yu Matsuki, Ryo Funayama, Keiko Nakayama & Masakado Kawata
What limits a species' distribution in the absence of physical barriers? Genetic load due to asymmetric gene flow and the absence of genetic variation due to lack of gene flow are hypothesized to constrain adaptation to novel environments in marginal populations, preventing range expansion. Here, we examined the genetic structure and geographic variation in morphological traits in two damselflies (Ischnura asiatica and I. senegalensis) along a latitudinal gradient in Japan, which is the distribution centre...

Data from: The direct cost of traumatic secretion transfer in hermaphroditic land snails: individuals stabbed with a love dart decrease lifetime fecundity

Kazuki Kimura & Satoshi Chiba
Several taxa of simultaneously hermaphroditic land snails exhibit a conspicuous mating behaviour, the so-called shooting of love darts. During mating, such land snail species transfer a specific secretion by stabbing a mating partner's body with the love dart. It has been shown that sperm donors benefit from this traumatic secretion transfer, because the secretions manipulate the physiology of a sperm recipient and increase the donors' fertilization success. However, it is unclear whether reception of dart...

Museomics for reconstructing historical floristic exchanges: Divergence of Stone Oaks across Wallacea

Joeri Strijk, Hoang Thi Bin Thi Bin, Ferry Slik, Rahayu Sukri, Yoshihisa Suyama, Shuichiro Tagane, Jan Wieringa, Tetsukazu Yahara & Damien Hinsinger
Natural history collections and tropical tree diversity are treasure troves of biological and evolutionary information, but its accessibility is impeded by several properties. DNA in historical specimens generally occurs in a highly fragmented state, complicating the recovery of high-grade genetic material for scientific studies. Our understanding of hyperdiverse, wide-spread tree assemblages suffers from patchy information on distributions, phenology and paucity of diagnostic characters. This prohibits rapid identification and the strengthening of taxonomic frameworks and in...

Genetic diversity and the origin of commercial plantation of Indonesian teak on Java Island

Eko Prasetyo, Widiyatno Widiyatno, Sapto Indrioko, Mohammad Na'iem, Tetsuya Matsui, Ayumi Matsuo, Yoshihisa Suyama & Yoshihiko Tsumura
Teak (Tectona grandis) has been widely planted in 70 tropical countries because of the utility and value of its wood. This species was introduced to Indonesia more than 100 years ago, and large plantations - covering 1.2 million ha – can be found on Java Island. However, little information currently exists about the genetic diversity and origin of these trees. We collected plant materials from three regions across Java Island (east, central, and west), and...

Data from: Cough reflex sensitivity and urge-to-cough deterioration in dementia with Lewy bodies

Takae Ebihara, Peijun Gui, Chika Ooyama, Koichi Kozaki & Satoru Ebihara
Cough, an important respiratory symptom, predominantly involves the brainstem, and the urge-to-cough is modulated by the cerebral cortex. Lewy body disease is associated with decreased cough reflex sensitivity and central respiratory chemosensitivity. Additionally, the insula, associated with the urge-to-cough, shows decreased activation and atrophy in dementia with Lewy bodies (DLB). We investigated the relationships between cognition and cough reflex and the urge-to-cough and compared the differences in responses of patients with DLB and other dementia...

Data from: Invasions of an obligate asexual daphnid species support the nearly neutral theory

Jotaro Urabe, Hajime Ohtsuki, Hiromoto Norimatsu & Takashi Makino
To verify the "nearly neutral theory (NNT)," the ratio of nonsynonymous to synonymous substitutions (dN/dS) was compared among populations of different species. To determine the validity of NNT, however, populations that are genetically isolated from each other but share the same selection agents and differ in size should be compared. Genetically different lineages of obligate asexual Daphnia pulex invading Japan from North America are an ideal example as they satisfy these prerequisites. Therefore, we analyzed...

Data from: Formin is associated with left-right asymmetry in the pond snail and the frog

Angus Davison, Gary S. McDowell, Jennifer M. Holden, Harriet F. Johnson, Georgios D. Koutsovoulos, M. Maureen Liu, Paco Hulpiau, Frans Van Roy, Christopher M. Wade, Ruby Banerjee, Fengtang Yang, Satoshi Chiba, John W. Davey, Daniel J. Jackson, Michael Levin & Mark L. Blaxter
While components of the pathway that establishes left-right asymmetry have been identified in diverse animals, from vertebrates to flies, it is striking that the genes involved in the first symmetry-breaking step remain wholly unknown in the most obviously chiral animals, the gastropod snails. Previously, research on snails was used to show that left-right signaling of Nodal, downstream of symmetry breaking, may be an ancestral feature of the Bilateria. Here, we report that a disabling mutation...

Data from: Molecular and pollen-based vegetation analysis in lake sediments from central Scandinavia

Laura Parducci, Irina Matetovici, Sonia L. Fontana, Keith D. Bennett, Yoshihisa Suyama, James Haile, Kurt H. Kjær, Nicolaj K. Larsen, Andreas D. Drouzas, Eske Willerslev & Kurt H. Kjaer
Plant and animal biodiversity can be studied by obtaining DNA directly from the environment. This new approach in combination with the use of generic barcoding primers (metabarcoding) has been suggested as complementary or alternative to traditional biodiversity monitoring in ancient soil sediments. However, the extent to which metabarcoding truly reflects plant composition remains unclear, as does its power to identify species with no pollen or macrofossil evidence. Here, we compared pollen-based and metabarcoding approaches to...

Data from: Spatial distribution of flower color induced by interspecific sexual interaction

Yuma Takahashi, Masakado Kawata & Koh-Ichi Takakura
Understanding the mechanisms shaping the spatiotemporal distribution of species has long been a central concern of ecology and evolutionary biology. Contemporary patterns of plant assemblies suggest that sexual interactions among species, i.e., reproductive interference, lead to the exclusive distributions of closely related species that share pollinators. However, the fitness consequences and the initial ecological/evolutionary responses to reproductive interference remain unclear in nature, since reproductive isolation or allopatric distribution has already been achieved in the natural...

Data from: Time-dependent decline of body-specific attention to the paretic limb in chronic stroke patients

Naoki Aizu, Yutaka Oouchida & Shin-Ichi Izumi
Objective: To examine whether reduced body-specific attention to paretic limb is found in chronic stroke patients in the time-dependent manner. Methods: Twenty-one patients with chronic hemiparesis (10 left and 11 right hemiparesis) after subcortical stroke and 18 age-matched healthy controls were recruited in this study. Standard neuropsychological examinations showed no clear evidence of spatial neglect in all patients. In order to quantitatively measure the spatial attention to paretic hand, a visual detection task for detecting...

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  • Tohoku University
  • University of Tokyo
  • Kyoto University
  • National Institute of Genetics
  • Ryukoku University
  • National Institute for Environmental Studies
  • University of Hyogo
  • Forestry and Forest Products Research Institute
  • National Museum of Nature and Science
  • Kyushu University