說明
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.
資料紀錄
此資源出現紀錄的資料已發佈為達爾文核心集檔案（DwC-A），其以一或多組資料表構成分享生物多樣性資料的標準格式。 核心資料表包含 825 筆紀錄。
亦存在 1 筆延伸集的資料表。延伸集中的紀錄補充核心集中紀錄的額外資訊。 每個延伸集資料表中資料筆數顯示如下。
此 IPT 存放資料以提供資料儲存庫服務。資料與資源的詮釋資料可由「下載」單元下載。「版本」表格列出此資源的其它公開版本，以便利追蹤其隨時間的變更。
版本
以下的表格只顯示可公開存取資源的已發布版本。
如何引用
研究者應依照以下指示引用此資源。:
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
權利
研究者應尊重以下權利聲明。:
此資料的發布者及權利單位為 National Institute of Genetics, ROIS。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.
GBIF 註冊
此資源已向GBIF註冊，並指定以下之GBIF UUID: 12bcc17a-9eb7-4377-96df-1a2135900550。 National Institute of Genetics, ROIS 發佈此資源，並經由GBIF Japan同意向GBIF註冊成為資料發佈者。
關鍵字
Occurrence; Specimen; chironomid; DNA barcoding; farm pond; freshwater biodiversity; molecular species delimitation
聯絡資訊
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- 元數據提供者 ●
- 出處
- 內容提供者 ●
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- 連絡人
- 程式設計師
地理涵蓋範圍
Hyogo, Japan
| 界定座標範圍 | 緯度南界 經度西界 [34.72, 134.808], 緯度北界 經度東界 [34.958, 135.027] |
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分類群涵蓋範圍
1 family (Chironomidae) including 20 genus of chironomids
| Family | Chironomidae |
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| Genus | Ablabesmyia, Benthalia, Chironomus, Corynoneura, Cricotopus, Dicrotendipes, Endochironomus, Glyptotendipes, Microchironomus, Nilodorum, Parachironomus, Paratanytarsus, Polypedilum, Procladius, Propsilocerus, Psectrocladius, Psectrotanypus, Sergentia, Tanypus, Tanytarsus |
時間涵蓋範圍
| 起始日期 / 結束日期 | 2012-05-23 / 2012-09-15 |
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計畫資料
無相關描述
| 計畫名稱 | Diversity and habitat preferences of insects of the family Chironomidae investigated with DNA barcoding |
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| 經費來源 | Grant Number 24241078, Grants-in-Aid for Scientific Research (KAKENHI), Japan Society for the Promotion of Science. |
| 研究區域描述 | 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. |
| 研究設計描述 | 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. |
參與計畫的人員:
取樣方法
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.
| 研究範圍 | Larvae of chironomid species were collected from 20 ponds in Hyogo, Japan in May and September 2012. |
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| 品質控管 | 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. |
方法步驟描述:
- 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.
- 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).
- 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.
引用文獻
- 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.
- 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.
- GBIF Secretariat (2022). GBIF backbone taxonomy. Checklist dataset https://doi.org/10.15468/39omei accessed via. GBIF.org on 2022-04-08.
- Japan Chironomid Workshop (Nippon-Yusurika Kenkyukai). (2010) Chironomidae of Japan. Bunichi Sogo Shuppan, Tokyo.
- 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
- 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
額外的詮釋資料
| 替代的識別碼 | 12bcc17a-9eb7-4377-96df-1a2135900550 |
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| https://gbif.jp/ipt/resource?r=nies_pond_chironomid |