100 Works

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: 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...

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: 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: 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...

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: 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...

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,...

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,...

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...

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...

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...

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...

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...

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: 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: 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: Sex chromosome turnover contributes to genomic divergence between incipient stickleback species

Kohta Yoshida, Takashi Makino, Katsushi Yamaguchi, Shuji Shigenobu, Mitsuyasu Hasebe, Masakado Kawata, Manabu Kume, Seiichi Mori, Catherine L. Peichel, Atsushi Toyoda, Asao Fujiyama & Jun Kitano
Sex chromosomes turn over rapidly in some taxonomic groups, where closely related species have different sex chromosomes. Although there are many examples of sex chromosome turnover, we know little about the functional roles of sex chromosome turnover in phenotypic diversification and genomic evolution. The sympatric pair of Japanese threespine stickleback (Gasterosteus aculeatus) provides an excellent system to address these questions: the Japan Sea species has a neo-sex chromosome system resulting from a fusion between an...

Data from: Divergence before and after the isolation of islands: phylogeography of the Bradybaena land snails on the Ryukyu Islands of Japan

Takahiro Hirano, Yuichi Kameda, Takumi Saito & Satoshi Chiba
Aim: Vicariance events have been proposed as a major source of lineage divergence on continental islands, whereas dispersal events followed by isolation have been proposed as the major cause on oceanic islands. However, organisms on continental islands may include taxa with characteristics similar to those on oceanic islands. Lineage divergence unassociated with the geological events that separated islands may also have occurred. This study addresses these possibilities through morphological and molecular phylogeographic analyses of land...

Data from: Simulation of the nodal flow of mutant embryos with small number of cilia: comparison of mechanosensing and vesicle transport hypotheses

Toshihiro Omori, Katja Winter, Kyosuke Shinohara, Hiroshi Hamada & Takuji Ishikawa
Left-right (L-R) asymmetry in the body plan is determined by nodal flow in vertebrate embryos. Shinohara et al. used Dpcd and Rfx3 mutant mouse embryos and showed that only a few cilia were sufficient to achieve L-R asymmetry. However, the mechanism underlying the breaking of symmetry by such weak ciliary flow is unclear. The flow-mediated signals related to L-R asymmetry have not been clarified; there are two models for L-R symmetry breaking: vesicle transport and...

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...

Data from: Habitat filtering determines the functional niche occupancy of plant communities worldwide

Yuanzhi Li, Bill Shipley, Jodi N. Price, Vinícius De L. Dantas, Riin Tamme, Mark Westoby, Andrew Siefert, Brandon S. Schamp, Marko J. Spasojevic, Vincent Jung, Daniel C. Laughlin, Sarah J. Richardson, Yoann Le Bagousse-Pinguet, Christian Schöb, Antonio Gazol, Honor C. Prentice, Nicolas Gross, Jacob Overton, Marcus V. Cianciaruso, Frédérique Louault, Chiho Kamiyama, Tohru Nakashizuka, Kouki Hikosaka, Takehiro Sasaki, Masatoshi Katabuchi … & Marco A. Batalha
How the patterns of niche occupancy vary from species-poor to species-rich communities is a fundamental question in ecology that has a central bearing on the processes that drive patterns of biodiversity. As species richness increases, habitat filtering should constrain the expansion of total niche volume, while limiting similarity should restrict the degree of niche overlap between species. Here, by explicitly incorporating intraspecific trait variability, we investigate the relationship between functional niche occupancy and species richness...

Data from: UV bullseye contrast of Hemerocallis flowers attracts hawkmoths but not swallowtail butterflies

Shun K. Hirota, Nozomu Miki, Akiko A. Yasumoto & Tetsukazu Yahara
The colour and patterns of animal-pollinated flowers are known to have effects on pollinator attraction. In this study, the relative importance of flower colour and colour contrast patterns on pollinator attraction was examined in two pollinator groups, swallowtail butterflies and hawkmoths using two Hemerocallis species; butterfly-pollinated H. fulva and hawkmoth-pollinated H. citrina, having reddish and yellowish flowers in human vision, respectively. Flowers of both species have UV bullseye patterns, composed of UV-absorbing centres and UV-reflecting...

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...

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