10 Works

Data from: Large-scale metabarcoding analysis of epipelagic and mesopelagic copepods in the Pacific

Junya Hirai, Aiko Tachibana & Atsushi Tsuda
A clear insight into large-scale community structure of planktonic copepods is critical to understanding mechanisms controlling diversity and biogeography of marine taxa, owing to their high abundance, ubiquity, and sensitivity to environmental changes. Here, we applied a 28S metabarcoding approach to large-scale communities of epipelagic and mesopelagic copepods at 70 stations across the Pacific Ocean and three stations in the Arctic Ocean. Major patterns of community structure and diversity, influenced by water mass structures, agreed...

Data from: Modelling the potential impacts of climate change on the distribution of ichthyoplankton in the Yangtze Estuary, China

Zhixin Zhang, Stefano Mammola, Weiwei Xian & Hui Zhang
Aim: Species distribution models (SDMs) are an effective tool to explore the potential distribution of terrestrial, freshwater, and marine organisms; however, SDMs have been seldom used to model ichthyoplankton distributions and thus our understanding of how larval stages of fishes will respond to climate change is still limited. Here, we developed SDMs to explore potential impacts of climate change on habitat suitability of ichthyoplankton. Location: Yangtze Estuary, China Methods: Using long-term ichthyoplankton survey data and...

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: 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...

Intraspecific genetic variation matters when predicting seagrass distribution under climate change

Zi-Min Hu, Quan-Sheng Zhang, Jie Zhang, Kass Jamie, Mammola Stefano, Fresia Pablo, Draisma Stefano, Assis Jorge, Jueterbock Alexander, Yokota Masashi & Zhixin Zhang
Seagrasses play a vital role in structuring coastal marine ecosystems, but their distributional range and genetic diversity have declined rapidly over the past decades. In order to improve conservation of seagrass species, it is important to predict how climate change may impact their ranges. Such predictions are typically made with correlative species distribution models (SDMs), which can estimate a species’ potential distribution under present and future climatic scenarios given species’ presence data and climatic predictor...

Lineage-level distribution models lead to more realistic climate change predictions for a threatened crayfish

Zhixin Zhang, Jamie Kass, Stefano Mammola, Itsuro Koizumi, Xuecao Li, Kazunori Tanaka, Kousuke Ikeda, Toru Suzuki, Masashi Yokota & Nisikawa Usio
Aim: As climate change presents a major threat to biodiversity in the next decades, it is critical to assess its impact on species habitat suitability to inform biodiversity conservation. Species distribution models (SDMs) are a widely used tool to assess climate change impacts on species’ geographical distributions. As the term suggests, the species-level is the most commonly used taxonomic unit in SDMs. However, recently it has been demonstrated that SDMs considering taxonomic resolution below (or...

Data from: Population structure and persistence of Pacific herring following the Great Tohoku earthquake

Shuichi Kitada, Ryohei Yoshikai, Tomonari Fujita, Katsuyuki Hamasaki, Reiichiro Nakamichi & Hirohisa Kishino
We evaluated the effect of the Great Tohoku earthquake, which occurred on March 11, 2011 in Japan, on the genetic diversity and population structure of Pacific herring (Clupea pallasii). Pacific herring (n = 4466) were collected between 2003 and 2014 through more than 20 sampling events during spawning periods at nine spawning sites throughout the Pacific herring distribution range in Japan. We measured them and genotyped 3784 fish at five microsatellite loci. Following the tsunami,...

Data from: Incremental analysis of vertebral centra can reconstruct the stable isotope chronology of teleost fishes

Jun Matsubayashi, Yu Saitoh, Yutaka Osada, Yoshitoshi Uehara, Junko Habu, Tsuyoshi Sasaki & Ichiro Tayasu
1. Isotope analysis has high potential for understanding fish ecology and food-web structure in aquatic ecosystems. The utility of isotope analysis will be greatly improved if we can reconstruct the chronology of several isotopes at multiple growth stages of individual fish. However, no practical methods exist for reconstructing the chronology of light-element isotopes (e.g. δ13C, δ15N, δ34S, and Δ14C) in teleost fishes. Here, we present and test a new analytical approach for reconstructing the isotopic...

Data from: A key metabolic gene for recurrent freshwater colonization and radiation in fishes

Asano Ishikawa, Naoki Kabeya, Koki Ikeya, Ryo Kakioka, Jennifer N. Cech, Naoki Osada, Miguel C. Leal, Jun Inoue, Manabu Kume, Atsushi Toyoda, Ayumi Tezuka, Atsushi J. Nagano, Yo Y. Yamasaki, Yuto Suzuki, Tomoyuki Kokita, Hiroshi Takahashi, Kay Lucek, David Marques, Yusuke Takehana, Kiyoshi Naruse, Seiichi Mori, Oscar Monroig, Nemiah Ladd, Carsten J. Schubert, Blake Matthews … & Jun Kitano
Colonization of new ecological niches has triggered large adaptive radiations. Although some lineages have made use of such opportunities, not all do so. The factors causing this variation among lineages are largely unknown. Here, we show that deficiency in docosahexaenoic acid (DHA), an essential ω-3 fatty acid, can constrain freshwater colonization by marine fishes. Our genomic analyses revealed multiple independent duplications of the fatty acid desaturase gene Fads2 in stickleback lineages that subsequently colonized and...

Data and scripts from: Exploratory analysis of multi-trait coadaptations in the light of population history

Reiichiro Nakamichi, Shuichi Kitada & Hirohisa Kishino
During the process of range expansion, populations encounter a variety of environments. They respond to the local environments by modifying their mutually interacting traits. Common approaches of landscape analysis include first focusing on the genes that undergo diversifying selection or directional selection in response to environmental variation. To understand the whole history of populations, it is ideal to capture the history of their range expansion with reference to the series of surrounding environments and to...

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  • Tokyo University of Marine Science and Technology
  • University of Tokyo
  • Okinawa Institute of Science and Technology
  • Hokkaido University
  • Fisheries Research Agency
  • Chinese Academy of Sciences
  • Gifu Kyoritsu University
  • Fred Hutchinson Cancer Research Center
  • Swiss Federal Institute of Aquatic Science and Technology
  • University of California System