13 Works

Data from: A metagenetic approach for revealing community structure of marine planktonic copepods

Junya Hirai, Mikiko Kuriyama, Tadafumi Ichikawa, Kiyotaka Hidaka & Atsushi Tsuda
Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We determined an appropriate similarity threshold for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) using an artificial community containing 33 morphologically identified species. The 99% similarity threshold had high species-level resolution for MOTU clustering...

Data from: Efficient inference of recombination hot regions in bacterial genomes

Koji Yahara, Xavier Didelot, M Azim. Ansari, Samuel K. Sheppard & Daniel Falush
In eukaryotes, detailed surveys of recombination rates have shown variation at multiple genomic scales and the presence of “hotspots” of highly elevated recombination. In bacteria, studies of recombination rate variation are less developed, in part because there are few analysis methods that take into account the clonal context within which bacterial evolution occurs. Here we focus in particular on identifying “hot regions” of the genome where DNA is transferred frequently between isolates. We present a...

Data from: Molecular and morphological evidence of hybridization between native Ruditapes philippinarum and the introduced Ruditapes form in Japan

Shuichi Kitada, Chie Fujikake, Yoshiho Asakura, Hitomi Yuki, Kaori Nakajima, Kelley M. Vargas, Shiori Kawashima, Katsuyuki Hamasaki & Hirohisa Kishino
Marine aquaculture and stock enhancement are major causes of the introduction of alien species. A good example of such an introduction is the Japanese shortneck clam Ruditapes philippinarum, one of the most important fishery resources in the world. To meet the domestic shortage of R. philippinarum caused by depleted catches, clams were imported to Japan from China and the Korean peninsula. The imported clam is an alien species that has a very similar morphology, and...

Data from: Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor

Maude W. Baldwin, Yasuka Toda, Tomoya Nakagita, Mary J. O'Connell, Kirk C. Klasing, Takumi Misaka, Scott V. Edwards & Stephen D. Liberles
Sensory systems define an animal's capacity for perception and can evolve to promote survival in new environmental niches. We have uncovered a noncanonical mechanism for sweet taste perception that evolved in hummingbirds since their divergence from insectivorous swifts, their closest relatives. We observed the widespread absence in birds of an essential subunit (T1R2) of the only known vertebrate sweet receptor, raising questions about how specialized nectar feeders such as hummingbirds sense sugars. Receptor expression studies...

Data from: Genetic effects of marine stock enhancement: a case study based on the highly piscivorous Japanese Spanish mackerel

Kaori Nakajima, Shuichi Kitada, Yoko Habara, Shoko Sano, Emi Yokoyama, Takuma Sugaya, Akio Iwamoto, Hirohisa Kishino & Katsuyuki Hamasaki
We used a before–after control–impact design to quantify the genetic effects of the large piscivorous Japanese Spanish mackerel (Scomberomorus niphonius) stock enhancement program on wild populations in the Seto Inland Sea. Samples of 1424 wild and 230 hatchery fish collected from 13 sites around Japan were genotyped using five microsatellite markers. A total of 758 wild and 103 hatchery fish were sequenced for the mitochondrial DNA D-loop region. The population structure of Japanese Spanish mackerel...

Data from: Antennal lobe organization and pheromone usage in bombycid moths

Shigehiro Namiki, Takaaki Daimon, Chika Iwatsuki, Toru Shimada & Ryohei Kanzaki
We investigated the neuroanatomy of the macroglomerular complex, which is dedicated for sex pheromone processing, in five species belonging to the subfamily Bombycinae, Ernolatia moorei, Trilocha varians, Rondotia menciana, Bombyx mandarina, and Bombyx mori. The glomerulus located at the dorsal-most part of the olfactory center shows the largest volume in most of the moth species studied thus far. Such normal glomerular organization has been observed in E. moorei and T. varians, which use a two-component...

Data from: Mutual stabilization of rhythmic vocalization and whole-body movement

Kohei Miyata & Kazutoshi Kudo
The current study investigated the rhythmic coordination between vocalization and whole-body movement. Previous studies have reported that spatiotemporal stability in rhythmic movement increases when coordinated with a rhythmic auditory stimulus or other effector in a stable coordination pattern. Therefore, the present study conducted two experiments to investigate (1) whether there is a stable coordination pattern between vocalization and whole-body movement and (2) whether a stable coordination pattern reduces variability in whole-body movement and vocalization. In...

Data from: Evolutionary renovation of L/M opsin polymorphism confers a fruit discrimination advantage to ateline New World monkeys

Yoshifumi Matsumoto, Chihiro Hiramatsu, Yuka Matsushita, Norihiro Ozawa, Ryuichi Ashino, Makiko Nakata, Satoshi Kasagi, Anthony Di Fiore, Colleen Schaffner, Filippo Aureli, Amanda D. Melin, Shoji Kawamura & Colleen M. Schaffner
New World monkeys exhibit prominent color vision variation due to allelic polymorphism of the long-to-middle wavelength (L/M) opsin gene. The known spectral variation of L/M opsins in primates is broadly determined by amino acid composition at three sites: 180, 277 and 285 (the “three-sites” rule). However, two L/M opsin alleles found in the black-handed spider monkeys (Ateles geoffroyi) are known exceptions, presumably due to novel mutations. The spectral separation of the two L/M photopigments is...

Data from: Building a responsive teacher: how temporal contingency of gaze interaction influences word learning with virtual tutors

Hanju Lee, Yasuhiro Kanakogi & Kazuo Hiraki
Animated pedagogical agents are lifelike virtual characters designed to augment learning. A review of developmental psychology literature led to the hypothesis that the temporal contingency of such agents would promote human learning. We developed a Pedagogical Agent with Gaze Interaction (PAGI), an experimental animated pedagogical agent that engages in gaze interaction with students. In this study, university students learned words of a foreign language, with temporally contingent PAGI (live group) or recorded version of PAGI...

Data from: The Kuroshio Current influences genetic diversity and population genetic structure of a tropical seagrass, Enhalus acoroides

Yuichi Nakajima, Yu Matsuki, Chunlan Lian, Miguel D. Fortes, Wilfredo H. Uy, Wilfredo L. Campos, Masahiro Nakaoka & Kazuo Nadaoka
Information on genetic diversity and differentiation of seagrass populations is essential for the conservation of coastal ecosystems. However, little is known about the seagrasses in the Indo-West Pacific Ocean, where the world's highest diversity of seagrasses occurs. The influence of sea currents on these populations is also unknown. We estimated the genetic diversity and population genetic structure and identified reproductive features in Enhalus acoroides populations from the Yaeyama Islands, Hainan Island and the Philippines. The...

Data from: Oceanic barriers promote language diversification in the Japanese Islands

Sean Lee & Toshikazu Hasegawa
Good barriers make good languages. Scholars have long speculated that geographical barriers impede linguistic contact between speech communities, and promote language diversification in a manner similar to the process of allopatric speciation. This hypothesis, however, has seldom been tested systematically and quantitatively. Here we adopt methods from evolutionary biology and attempt to quantify the influence of oceanic barriers on the degree of lexical diversity in the Japanese Islands. Measuring the degree of beta diversity from...

Data from: Natural allelic variations of xenobiotic metabolizing enzymes affect sexual dimorphism in Oryzias latipes

Takafumi Katsumura, Shoji Oda, Shigeki Nakagome, Tsunehiko Hanihara, Hiroshi Kataoka, Hiroshi Mitani, Shoji Kawamura & Hiroki Oota
Sexual dimorphisms, which are phenotypic differences between males and females, are driven by sexual selection. Interestingly, sexually selected traits show geographical variations within species despite strong directional selective pressures. This paradox has eluded many evolutionary biologists for some time, and several models have been proposed (e.g. ‘indicator model’ and ‘trade-off model’). However, disentangling which of these theories explains empirical patterns remains difficult, because genetic polymorphisms that cause variation in sexual differences are still unknown. In...

Data from: Female polyandry and size-assortative mating in isolated local populations of the Japanese common toad Bufo japonicus

Kazuko Hase & Masakazu Shimada
In anurans, female polyandry under male harassment is distributed across taxa because of external aquatic fertilisation. According to the sexual selection theory, male–male competition for access to females is affected by the operational sex ratio (OSR) and population density. The Japanese common toad, Bufo japonicus, is widespread in mainland Japan, and like the European common toad, B. bufo, it engages in explosive breeding. We observed the breeding behaviour of B. japonicus in isolated local populations...

Registration Year

  • 2014

Resource Types

  • Dataset


  • University of Tokyo
  • Fisheries Research Agency
  • Tokyo University of Marine Science and Technology
  • Kitasato University
  • The University of Texas at Austin
  • Kyushu University
  • Tokyo Institute of Technology
  • National Institute of Agrobiological Sciences
  • Mindanao State University Naawan
  • Washington University in St. Louis