Photo images, 3D models and CT scanned data of loaches (Botiidae, Cobitidae and Nemacheilidae) of Japan

Yuichi Kano1, Jun Nakajima2, Takeshi Yamasaki3, Jyun-ichi Kitamura4, Ryoichi Tabata5

1 Kyushu University, 744 Motooka, Nishi-ku, 8190395, Fukuoka-shi, Japan; 2 Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, 8180135, Dazaifu, Japan; 3 Yamashina Institute for Ornithology, Japan, 115 Konoyama, 2701145, Abiko-shi, Japan; 4 Mie Prefectural Museum, 3060 Isshinden-kōzubeta, 5140061, Tsu-shi, Japan; 5 Lake Biwa Museum, 1091 Oroshimocho, 5250001, Kusatsu, Japan

Corresponding author(s): Yuichi Kano (kano@species.jp)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

Kano Y (2021): Photo images, 3D models and CT scanned data of loaches (Botiidae, Cobitidae and Nemacheilidae) of Japan. v1.9. Biodiversity Data Journal. Dataset/Occurrence. http://ipt.pensoft.net/resource?r=jp_loaches_3dct_models&v=1.9

Abstract

Loach is one of the major cypriniform fishes in freshwater habitats of Japan, being recognized 23 described species/subspecies and 12 undescribed/undecides clades (Nakajima and Uchiyama 2017) (http://ffish.asia/loachesOfJapan). As well as molecular genetic research (Kitagawa et al. 2001a, Kitagawa et al. 2001b, Kitagawa et al. 2003a, Kitagawa et al. 2003b, Kitagawa et al. 2005, Suzawa 2006, Morishima et al. 2008, Saitoh et al. 2010, Kano et al. 2011, Miyazaki et al. 2011, Shimizu et al. 2011, Kano et al. 2012, Nakajima 2012, Nakajima 2016, Nakajima and Suzawa 2016, Nakajima and Uchiyama 2017), morphological examinations are needed for further development of loach study. Digital archiving of fish specimens is one of the progressive challenges in ichthyology for open science (Kanagawa Prefectural Museum of Natural History and National Museum of Nature and Science 1998, Berquist et al. 2012, Kano et al. 2013, Kano et al. 2016). This paper aimed to online publish photo images, 3D models and CT scanned data of all the known taxa/clades of loaches inhabiting in Japan (http://ffish.asia/loachesOfJapan3D) for the advances of loach study and ichthyology, and furthermore as a challenge of open science for public interests of biology.

Keywords: 3D model; Anatomy; Bone; CT scan; Digital archiving; Fish specimen; Freshwater fishes of Japan; GBIF; Holotype; Loach; Morphology; Open science; Paratype; Skeleton; Undescribed species, Inventorythematic

Project details

Project title: N/A
Personnel: Yuichi Kano
Funding: This work was partially supported by JSPS KAKENHI Grant Number 18HP8029.

Data published through GBIF: http://ipt.pensoft.net/resource?r=jp_loaches_3dct_models

Taxonomic coverage

Taxonomic ranks
Kingdom: Animalia
Phylum: Chordata
Subphylum: Craniata
Class: Osteichthyes
Order: Cypriniformes
Family: Botiidae, Cobitidae, Nemacheilidae
Species: Parabotia curtus, Cobitis kaibarai, Cobitis magnostriata, Cobitis matsubarae, Cobitis sp. "yamato" complex Type A, Cobitis sakahoko, Cobitis shikokuensis, Cobitis sp. BIWAE type A, Cobitis sp. BIWAE type B, Cobitis sp. BIWAE type C, Cobitis sp. BIWAE type D, Cobitis takatsuensis, Cobitis takenoi, Misgurnus sp. (Clade A), Misgurnus anguillicaudatus (Clade B1), Misgurnus anguillicaudatus (Clade B2), Misgurnus anguillicaudatus (jindai), Misgurnus sp. IR, Misgurnus sp. OK, Misgurnus dabryanus, Niwaella delicata, Barbatula oreas, Lefua costata, Lefua echigonia, Lefua nikkonis, Lefua sp. 1, Lefua sp. 2
Subspecies: Cobitis minamorii minamorii, Cobitis minamorii oumiensis, Cobitis minamorii saninensis, Cobitis minamorii tokaiensis, Cobitis minamorii yodoensis, Cobitis striata fuchigamii, Cobitis striata hakataensis, Cobitis striata striata
Common names: Animals, Chordates, Vertebrat es and hagfishes, Bony fishes and tetrapods, Carps, loaches, minnows and relatives, Botiid loach, "Ayumodoki", True loaches, "Ariake-suji-shima-dojyô", "Oogata-suji-shima-dojyô", "Yamato-shima-dojyô", "Yamato-shima-dojyô" (Type A), "San'yô-kogata-suji-shima-dojyô", "Biwa-kogata-suji-shima-dojyô", "San'in-kogata-suji-shima-dojyô", "Tôkai-kogata-suji-shima-dojyô", "Tôkai-kogata-suji-shima-dojyô", "Oyodo-shima-dojyô", "Hina-ishi-dojyô", "Oo-shima-dojyô", "Nishi-shima-dojyô", "Higashi-shima-dojyô", "Tosas-shima-dojyô", "Onga-suji-shima-dojyô", "Hakata-suji-shima-dojyô", "Chûgata-suji-shima-dojyô", "Ishi-dojyô", "Tango-suji-shima-dojyô", "Kita-dojyô", "Dojyô" (Japan clade), "Dojyô" (China clade), "Jindai-dojyô", "Shinobi-dojyô", "Hyoumon-dojyô", "Kara-dojyô", "Ajime-dojyô", Stone loaches, "Fuku-dojyô", "Hime-dojyô", "Hotoke-dojyô", "Ezo-hotoke-dojyô", "Nagare-hotoke-dojyô", "Tôkai-nagare-hotoke-dojyô"

Spatial coverage

General spatial coverage: Inland water habitats of Japan.
Coordinates: 23°0'0''N and 46°0'0''N Latitude; 123°0'0''E and 150°0'0''E Longitude 

Temporal coverage: June 6, 1954 - December 15, 2017

Natural collections description

Collection name: JNC/JNCP (J. Nakajima's personal collection)
Natural collections description

Collection name: KPM (Kanagawa Prefectural Museum of Natural History)
Natural collections description

Collection name: LBM (Lake Biwa Museum)
Natural collections description

Collection name: MPM/MPMQ (Mie Prefectural Museum)
Natural collections description

Collection name: OMNH (Osaka Museum of Natural History)
Natural collections description

Collection name: QUYK (Y. Kano's personal collection)
Natural collections description

Collection name: TKPM (Tokushima Prefectural Museum)
Specimen preservation method: Formalin

Methods

Method step description: Photo images were taken in the fields by capturing individuals (Kano and Nakajima 2014) and/or by snorkeling. The formalin-fixed specimens were also photographed in the laboratory followed by CT scanning (Aloka Latheta LCT-200, Hitachi, Ltd.). 3D surface (CT value: -400 to -40) and skeletal (CT value: 5 to 200) models were extracted from the CT data. The CT data in raw file format was also stored and available on the web.
Study extent description: Specimens of loaches of Japan were collected from personal collections and museums.
Sampling description: The specimens were generally captured by a hand-net in the fields.

Datasets

Dataset description
Object name: Darwin Core Archive Photo images, 3D models and CT scanned data of loaches (Botiidae, Cobitidae and Nemacheilidae) of Japan
Character encoding: UTF-8
Format name: Darwin Core Archive format
Format version: 1.0
Distribution: http://ipt.pensoft.net/archive.do?r=jp_loaches_3dct_models
Publication date of data: 2021-08-31
Language: English
Licences of use: Creative Commons Attribution Non Commercial (CC-BY-NC) 4.0 License

External datasets

Dataset description
Object name: loachesOfJapan
Character encoding: UTF-8
Format name: html; jpg
Distribution: http://ffish.asia/loachesOfJapan

Dataset description
Object name: loachesOfJapan3D
Character encoding: UTF-8
Format name: html; Wavefront object format (.obj); CT dicom file (.dcm)
Distribution: http://ffish.asia/loachesOfJapan3D

Metadata language: English
Date of metadata creation: 2018-02-11
Hierarchy level: Dataset