Biodiversity Data Journal : Data Paper (Biosciences)
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Corresponding author: Yuichi Kano (kano@species.jp)
Academic editor: Yasen Mutafchiev
Received: 29 Apr 2018 | Accepted: 11 Jun 2018 | Published: 06 Jul 2018
© 2018 Yuichi Kano, Jun Nakajima, Takeshi Yamasaki, Jyun-ichi Kitamura, Ryoichi Tabata
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation: Kano Y, Nakajima J, Yamasaki T, Kitamura J, Tabata R () Photo images, 3D models and CT scanned data of loaches (Botiidae, Cobitidae and Nemacheilidae) of Japan. . https://doi.org/
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Loach is one of the major cypriniform fishes in freshwater habitats of Japan; 35 taxa/clades have, until now, been recognised. Parallel to genetic studies, morphological examinations are needed for further development of loach study, eventually ichthyology and fish biology. Digital archiving, concerning taxonomy, ecology, ethology etc., is one of the progressive challenges for the open science of biology. This paper aimed to online publish photo images, 3D models and CT scanned data of all the known clades of loaches inhabiting Japan (103 individuals in total with several type specimens), contributing to ichthyology and public interest of biodiversity/biology.
Photo images, 3D models and CT scanned data of all the known 35 taxa/clades of loaches inhabiting in Japan were online published at http://ffish.asia/loachesOfJapan and http://ffish.asia/loachesOfJapan3D.
3D model; Anatomy; Bone; CT scan; Digital archiving; Fish specimen; Freshwater fishes of Japan; GBIF; Holotype; Loach; Morphology; Open science; Paratype; Skeleton; Undescribed species
Loach is one of the major cypriniform fishes in freshwater habitats of Japan, being recognised with 23 described species/subspecies and 12 undescribed/undecided clades (
This research aims to
1) list all the known taxa/clades of loaches inhabiting Japan with photo images (http://ffish.asia/loachesOfJapan) and
2) digitalise the specimens of each taxa/clades by 3D models and CT scanning (http://ffish.asia/loachesOfJapan3D).
The dataset was also registered on GBIF (http://ipt.pensoft.net/resource?r=jp_loaches_3dct_models)
Photo images and specimens of loaches of Japan were taken in the field and borrowed from museums (see "Collection data").
The specimens were generally captured by a hand-net in the field. All the specimens were fixed in 10% formalin and preserved in 70% ethanol.
Photo images were taken in the field by capturing individuals (Fig.
A photo image of an individual of Parabotia curtus in a makeshift aquarium at a wild habitat.
A photo image of Cobitis sakahoko in the wild, under cloudy water by volcanic ash of Mt. Kirishima.
An old specimen of Misgurnus anguillicaudatus (Jindai-dojyô) (MPMQ-JJ1), an uncertain local clade that is already extinct.
A 3D model of the surface of Misgurnus anguillicaudatus (Clade B1) (JNC342).
A 3D skeletal model of a paratype of Cobitis striata fuchigamii (MPM-Fi1501).
CT scanned data of Barbatula oreas (JNC256).
A movie for CT scanned data of Cobitis minamorii yodoensis (OMNH-P45848), changing the camera angle and CT value.
Inland water habitats of Japan.
23 and 46 Latitude; 150 and 123 Longitude.
This paper includes all the known 35 loach taxa/clades (103 specimens) in Japan, of which 12 clades have still been undescribed or are uncertain.
Type specimens: The dataset includes nine type specimens as below.
Holotype: MPM-Fi1507 (Cobitis minamorii tokaiensis).
Paratypes: MPM-Fi1501 (Cobitis striata fuchigamii); MPM-Fi1502 (Cobitis striata hakataensis); MPM-Fi1503 (Cobitis kaibarai); MPM-Fi1504 (Cobitis magnostriata); MPM-Fi1505 (Cobitis minamorii minamorii); MPM-Fi1506 (Cobitis minamorii oumiensis); MPM-Fi1508 (Cobitis minamorii tokaiensis); MPM-Fi1509 (Cobitis minamorii saninensis).
Undescribed/uncertain clades: Below, we interpret the 12 undescribed/uncertain clades.
Twenty taxa of genus Cobitis have been hitherto known in Japan (
The situation about "Misgurnus anguillicaudatus" is rather complicated. Six taxa/clades of Misgurnus anguillicaudatus species complex has been hitherto known in Japan, namely "A", "B1", "B2", "Jindai", "IR" and "OK". Misgurnus sp. (Clade A) is a native loach clade of Japan, although the distribution is limited to northern parts such as Hokkaido and eastern Honshu (
Two Lefua species have still been left undescribed. Lefua sp. 1 is distributed amongst a narrow range of western Honshu, eastern Shikoku, Awaji Island and Shodo Island (
Non-native to Japan:
Misgurnus anguillicaudatus (Clade B2): Definite native range of M. anguillicaudatus (Clade B2) is still unclear, but it potentially inhabits China (
Misgurnus dabryanus: Native to China (
Lefua costata: Native to northern China (
IUCN rank and extinction: Japanese loaches are generally faced with extinction and a part of them are listed in the IUCN Red List. Two loaches have been unconfirmed for the last 20 years indicating extinction.
CR: Parabotia curtus
LC: "Misgurnus anguillicaudatus" that potentially includes Misgurnus sp. (Clade A), M. anguillicaudatus (Clade B1), M. anguillicaudatus (Clade B2), M. anguillicaudatus (Jindai), Misgurnus sp. IR and Misgurnus sp. OK.
Assumed to be extinct: Cobitis minamorii yodoensis; Misgurnus anguillicaudatus (Jindai).
Rank | Scientific Name | Common Name |
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kingdom | Animalia | Animals |
phylum | Chordata | Chordates |
subphylum | Craniata | Vertebrates and hagfishes |
class | Osteichthyes | Bony fishes and tetrapods |
subclass | Actinopterygii | Ray-finned fishes |
order | Cypriniformes | Carps, loaches, minnows and relatives |
family | Botiidae | Botiid loach |
species | Parabotia curtus | "Ayumodoki" |
family | Cobitidae | True loaches |
species | Cobitis kaibarai | "Ariake-suji-shima-dojyô" |
species | Cobitis magnostriata | "Oogata-suji-shima-dojyô" |
species | Cobitis matsubarae | "Yamato-shima-dojyô" |
species | Cobitis sp. "yamato" complex Type A | "Yamato-shima-dojyô" (Type A) |
subspecies | Cobitis minamorii minamorii | "San'yô-kogata-suji-shima-dojyô" |
subspecies | Cobitis minamorii oumiensis | "Biwa-kogata-suji-shima-dojyô" |
subspecies | Cobitis minamorii saninensis | "San'in-kogata-suji-shima-dojyô" |
subspecies | Cobitis minamorii tokaiensis | "Tôkai-kogata-suji-shima-dojyô" |
subspecies | Cobitis minamorii yodoensis | "Yodo-kogata-suji-shima-dojyô" |
species | Cobitis sakahoko | "Oyodo-shima-dojyô" |
species | Cobitis shikokuensis | "Hina-ishi-dojyô" |
species | Cobitis sp. BIWAE type A | "Oo-shima-dojyô" |
species | Cobitis sp. BIWAE type B | "Nishi-shima-dojyô" |
species | Cobitis sp. BIWAE type C | "Higashi-shima-dojyô" |
species | Cobitis sp. BIWAE type D | "Tosa-shima-dojyô" |
subspecies | Cobitis striata fuchigamii | "Onga-suji-shima-dojyô" |
subspecies | Cobitis striata hakataensis | "Hakata-suji-shima-dojyô" |
subspecies | Cobitis striata striata | "Chûgata-suji-shima-dojyô" |
species | Cobitis takatsuensis | "Ishi-dojyô" |
species | Cobitis takenoi | "Tango-suji-shima-dojyô" |
species | Misgurnus sp. (Clade A) | "Kita-dojyô" |
species | Misgurnus anguillicaudatus (Clade B1) | "Dojyô" (Japan clade) |
species | Misgurnus anguillicaudatus (Clade B2) | "Dojyô" (China clade) |
species | Misgurnus anguillicaudatus (Jindai) | "Jindai-dojyô" |
species | Misgurnus sp. IR | "Shinobi-dojyô" |
species | Misgurnus sp. OK | "Hyoumon-dojyô" |
species | Misgurnus dabryanus | "Kara-dojyô" |
species | Niwaella delicata | "Ajime-dojyô" |
family | Nemacheilidae | Stone loaches |
species | Barbatula oreas | "Fuku-dojyô" |
species | Lefua costata | "Hime-dojyô" |
species | Lefua echigonia | "Hotoke-dojyô" |
species | Lefua nikkonis | "Ezo-hotoke-dojyô" |
species | Lefua sp. 1 | "Nagare-hotoke-dojyô" |
species | Lefua sp. 2 | "Tôkai-nagare-hotoke-dojyô" |
Several specimens have no temporal information.
All the 35 known clades of loaches inhabiting Japan are listed with photo images. Below, the main 6 columns are listed;
Column label | Column description |
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Scientific name | Formal scientific name or tentative name |
Taxon | Taxonomical hierarchy (order/family/genus) |
Species image | Photo images of the species |
N | Number of specimen/occurence data |
Specimens/data distribution | Showing rough localities of the occurence on a map |
Other information | Other information such as Japanese name |
Surface/skeletal 3D models and CT scanned data are available for all the clades (103 individuals). To render the CT dicom files as a visual 3D volume, several free software are available. Below, the main 12 columns are listed;
Column label | Column description |
---|---|
Specimen/Data ID | ID for the specimen/occurence |
Images | Downloadable images/files of photos, 3D models and CT scanned data |
Species | Scientific name (or tentative name) of the specimen |
Taxon | Taxonomical hierarchy (order/family/genus) |
N | Number of the individual(s) |
DNA information | DNA sequence data if available |
Location | Description of the locality |
Specimens/data distribution | Showing rough localities of the occurence on a map |
Sample year/month/day | Temporal infomation of the sampling |
Japanese name | Japanese name |
English name | English name or roman phonetics for Japanese |
Comment | Other infomation such as sex, holotype, paratype etc. |
GBIF registered occurrence data for the specimens. Below, the main 10 columns are listed;
Column label | Column description |
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occurrenceID | Occurrence ID and URL |
basisOfRecord | The specific nature of the data record |
eventDate | The date-time or interval during which the specimen collected |
scientificName | Scientific name (or tentative name) of the specimen |
decimalLatitude | Rough value of decimal latitude |
decimalLongitude | Rough value of decimal longtitude |
verbatimLocality | Description of the locality |
typeStatus | Noted if the specimen is holotype or paratype |
sex | Discrimination of male or female, while some are unknown |
vernacularName | Japanese name |
We deeply appreciate Dr. Akihisa Iwata for help in taking photographs of Parabotia curtus. We are grateful to Mr. Mike Skinner for English proofreading. We also thank The Kyoto University Museum, Kanagawa Prefectural Museum of Natural History, Osaka Museum of Natural History and Tokushima Prefectural Museum for renting/loaning the specimens. This paper also includes partial results of studies funded by JSPS KAKENHI Grant Number 18HP8029 and Ministry of Agriculture, Forestry and Fisheries of Japan (Research Project for Biodiversity Assessment and Conservation for Sustainable Agriculture).
Yuichi Kano (manuscript writing, photographs and database/data management), Jun Nakajima (manuscript writing, photographs, identification and specimens provision), Taksehi Yamasaki (CT scanning), Jyun-ichi Kitamura (specimens provision) and Ryoichi Tabata (specimens provision).