DNA barcoding on chironomid specimens collected from ponds in Hyogo, Japan

最新バージョン National Institute of Genetics, ROIS によって公開 2022/06/15 National Institute of Genetics, ROIS
CC-BY 4.0

DwC-A形式のリソース データまたは EML / RTF 形式のリソース メタデータの最新バージョンをダウンロード:

DwC ファイルとしてのデータ ダウンロード 825 レコード English で (65 KB) - 更新頻度: not planned
EML ファイルとしてのメタデータ ダウンロード English で (20 KB)
RTF ファイルとしてのメタデータ ダウンロード English で (16 KB)


This dataset includes 825 chironomid specimen records collected from 20 ponds in Hyogo, Japan in May and September 2012. Specimens were identified to family, genus and species levels through DNA barcoding analysis for approximately 60 % of collected specimen samples, while species of 12 specimens were identified based on morphological identification solely. DNA sequences of COI mitochondrial gene of identified specimens were deposited in DNA Data Bank of Japan (DDBJ) with accession number of LC494722–LC495141.

データ レコード

この オカレンス(観察データと標本) リソース内のデータは、1 つまたは複数のデータ テーブルとして生物多様性データを共有するための標準化された形式であるダーウィン コア アーカイブ (DwC-A) として公開されています。 コア データ テーブルには、825 レコードが含まれています。

拡張データ テーブルは1 件存在しています。拡張レコードは、コアのレコードについての追加情報を提供するものです。 各拡張データ テーブル内のレコード数を以下に示します。

Occurrence (コア)

この IPT はデータをアーカイブし、データ リポジトリとして機能します。データとリソースのメタデータは、 ダウンロード セクションからダウンロードできます。 バージョン テーブルから公開可能な他のバージョンを閲覧でき、リソースに加えられた変更を知ることができます。





National Institute for Environmental Studies (2022) DNA barcoding on chironomid specimens collected from ponds in Hyogo, Japan. Version 1.2. National Institute for Environmental Studies. Dataset/Species occurrences. https://doi.org/10.15468/ez9xzh



パブリッシャーとライセンス保持者権利者は National Institute of Genetics, ROIS。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.


このリソースをはGBIF と登録されており GBIF UUID: 12bcc17a-9eb7-4377-96df-1a2135900550が割り当てられています。   GBIF Japan によって承認されたデータ パブリッシャーとして GBIF に登録されているNational Institute of Genetics, ROIS が、このリソースをパブリッシュしました。


Occurrence; Specimen; chironomid; DNA barcoding; farm pond; freshwater biodiversity; molecular species delimitation


Kenzi Takamura
  • データ提供者
  • メタデータ提供者
  • 最初のデータ採集者
  • 連絡先
Visiting Researcher
National Institute for Environmental Studies
16-2 Onogawa
305-8506 Tsukuba
Biodiversity Division
  • 連絡先
National Institute for Environmental Studies
Ryuhei Ueno
  • データ提供者
Senior Researcher Associate
National Institute for Environmental Studies
16-2 Onogawa
305-8506 Tsukuba
Natsuko I. Kondo
  • データ提供者
Senior Researcher
National Institute for Environmental Studies
16-2 Onogawa
305-8506 Tsukuba
Kako Ohbayashi
  • データ提供者
Chubu University
1200 Matsumoto-cho
487-8501 Kasugai
Kumiko Totsu
  • プログラマー
Specialist (Database engineer)
National Institute for Environmental Studies
16-2 Onogawa
305-8506 Tsukuba


Hyogo, Japan

座標(緯度経度) 南 西 [34.72, 134.808], 北 東 [34.958, 135.027]


1 family (Chironomidae) including 20 genus of chironomids

Family Chironomidae
Genus Ablabesmyia, Benthalia, Chironomus, Corynoneura, Cricotopus, Dicrotendipes, Endochironomus, Glyptotendipes, Microchironomus, Nilodorum, Parachironomus, Paratanytarsus, Polypedilum, Procladius, Propsilocerus, Psectrocladius, Psectrotanypus, Sergentia, Tanypus, Tanytarsus


開始日 / 終了日 2012-05-23 / 2012-09-15



タイトル Diversity and habitat preferences of insects of the family Chironomidae investigated with DNA barcoding
ファンデイング Grant Number 24241078, Grants-in-Aid for Scientific Research (KAKENHI), Japan Society for the Promotion of Science.
Study Area Description The farm ponds studied are located in the Banshu Plain of the Setonaikai Coast, Western Japan. They roughly range in the latitude of 34°43' to 34°58' and the longitude of 134°48' to 135°2'. In the Hyogo Prefecture where the ponds are located, there were over 55,000 farm ponds in 1950s, but over 4,500 ponds were lost mainly due to urban development by 1997. Recently, a rapid loss of farm ponds as a biodiversity habitat is continuing in this area.
研究の意図、目的、背景など(デザイン) This project is a part of the freshwater biodiversity research among farm ponds in the Banshu Plain of the Setonaikai Coast, Western Japan. These ponds have been built for agricultural irrigation, but now they are habitats for a wide variety of taxa originated from freshwater and its surrounding landscapes. This unique biodiversity has been threatened with recent urban development, so that the biodiversity research has been undertaken to reveal the present status as well as causes of dynamics (decline or increase) for a wide variety of freshwater taxa since the 1990s. The faunal and floral surveys of the research have been based on species identification of organisms by taxonomical specialists who were proficient in morphological characteristics of the species. Hence, the work has a fair amount of difficulties in delimitation of species which share common characteristics in key morphological features. This project adopts the methodology of molecular species delimitation, so that it enables to deepen the biodiversity analysis further, and is expected to promote the understanding and conservation of the biodiversity in the area.


Kenzi Takamura


Samples were collected from sediments using Ekman-Birge grab sampler (15 cm square in the mouth), and from aquatic weed stems (1m) with leaves by hands or aquatic weed sampler. The chironomids were sorted on ice in order to restrain degradation of DNA and preserved individually in 1.5 ml plastic tubes in a freezer for DNA analysis.

Study Extent Larvae of chironomid species were collected from 20 ponds in Hyogo, Japan in May and September 2012.
Quality Control Spelling of scientific names were checked against the GBIF Backbone Taxonomy (GBIF Secretariat 2022). Geographical coordinates were validated using GSI maps provided by Geospatial Information Authority of Japan.

Method step description:

  1. Morphological identification was performed during the sorting based on the morphological keys (e.g., Andersen et al., 2013; Japan Chironomid Workshop, 2010), and a small number of larvae with unique morphological characters were identified as species.
  2. DNA extraction and sequencing as well as species delimitation based on the sequences, were conducted as described in Takamura et al. (2021) and Takamura et al. (2017).
  3. Specimen data was organized into species occurrence data accompanied with DNA data using a MySQL database. A DDBJ link including accession number was stored in associatedSequences for both DDBJ registered and non-registered specimen records, as far as sharing the same sequences. Specimen records registered to DDBJ can be filtered by occurrenceRemarks. Coordinate uncertainty is represented by a half of the length of the major axis of each pond.


  1. Andersen, T., Ekrem, T., & Cranston, P. S. (2013) 1. The larvae of the Chironomidae (Diptera) of the Holarctic Region –Introduction. In T. P. Andersen, P. S. Cranston, & J. H. Elper (Eds.), Chironomidae of the Holarctic Region: Keys and diagnoses –Larvae (pp. 7–12). Insect Systematics & Evolution, Supplement 66.
  2. Folmer O., Black M., Hoeh W., Lutz R., Vrijenhoek R. (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294–299.
  3. GBIF Secretariat (2022). GBIF backbone taxonomy. Checklist dataset https://doi.org/10.15468/39omei accessed via. GBIF.org on 2022-04-08.
  4. Japan Chironomid Workshop (Nippon-Yusurika Kenkyukai). (2010) Chironomidae of Japan. Bunichi Sogo Shuppan, Tokyo.
  5. Takamura K., Ueno R., Kondo N.I., Ohbayashi K. (2021) Pond chironomid communities revealed by molecular species delimitation reflect eutrophication. Ecology and Evolution, 11, 4193–4204. https://doi.org/10.1002/ece3.7315 10.1002/ece3.7315
  6. Takamura, K., Ueno, R., Kondo, N.I., Ohbayashi, K. (2017) DNA-sequence-based species delimitation for larval chironomid samples collected from Japanese farm ponds. Japanese Journal of Limnology, 78, 35–43. https://doi.org/10.3739/rikusui.78.35. (in Japanese) 10.3739/rikusui.78.35


代替識別子 12bcc17a-9eb7-4377-96df-1a2135900550