說明
The dataset presented here includes detection of species in the Houdong River (猴洞坑) located in Jiaoxi Township, Yilan, Taiwan. Fieldwork was conducted on April 28th, 2022. The primary objective of this study was to determine the occurrence of species in riverine ecosystems through the use of environmental DNA methodology.
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 6,297 筆紀錄。
亦存在 4 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
請注意，此資料集為舊版本。 研究者應依照以下指示引用此資源。:
Hoh D (2023): eDNA along Houdong riverine zonation in Taiwan. v1.2. Taiwan Biodiversity Information Facility (TaiBIF). Dataset/Samplingevent. https://ipt.taibif.tw/resource?r=houdongkeng_water_edna&v=1.2
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 Taiwan Biodiversity Information Facility (TaiBIF)。 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: 2615342d-7349-4e75-ae34-cda6cb403e2e。 Taiwan Biodiversity Information Facility (TaiBIF) 發佈此資源，並經由Taiwan Biodiversity Information Facility同意向GBIF註冊成為資料發佈者。
關鍵字
SamplingEvent
聯絡資訊
- 元數據提供者 ●
- 出處 ●
- 連絡人
http://orcid.org/0000-0002-7810-1034
- 連絡人
地理涵蓋範圍
Houdong River (猴洞坑), Jiaoxi Township, Yilan County, Taiwan
| 界定座標範圍 | 緯度南界 經度西界 [24.824, 121.768], 緯度北界 經度東界 [24.871, 121.846] |
|---|
分類群涵蓋範圍
We detected eukaryotic organisms in the water samples using the cytochrome oxidase subunit 1 (COI) mitochondrial gene. A total of 2,736 operational taxonomic units (OTUs) were identified, but only 421 of these could be successfully assigned to a taxonomic group at (at least) the kingdom level.
| Domain | Eukaryota |
|---|---|
| Kingdom | Animalia, Chromista, Fungi, Plantae, Protozoa |
| Phylum | Amoebozoa, Bryophyta, Cryptophyta, Nemertea, Sulcozoa, Annelida, Bryozoa, Gastrotricha, Ochrophyta, Tracheophyta, Arthropoda, Chaetognatha, Glomeromycota, Oomycota, Zygomycota, Ascomycota, Chlorophyta, Haptophyta, Platyhelminthes, Basidiomycota, Chordata, Mollusca, Rhodophyta, Blastocladiomycota, Cnidaria, Mycetozoa, Rotifera |
時間涵蓋範圍
| 起始日期 | 2022-04-28 |
|---|
計畫資料
無相關描述
| 計畫名稱 | Environmental DNA-based biodiversity profiling along Houdong riverine zonation in Taiwan |
|---|
參與計畫的人員:
- 作者
- 作者
取樣方法
Surface water was collected from each site on the same day, and various water quality parameters were measured on site, including temperature, pH, dissolved oxygen (DO) content, turbidity, and salinity, with three replicate measurements taken for each parameter. Samples were processed at the Marine Research Station of the Institute of Cellular and Organismic Biology and the Biodiversity Research Centre at Academia Sinica in Taiwan. To prepare the samples for eDNA metabarcoding analysis, each water sample was filtered twice. The first filtration step involved using a 75 µm pore size sieve to remove larger materials, such as debris. Next, a 0.22 μm PES filter membrane with a vacuum pump was used to collect eDNA from the filtered water. Two PES filter membranes were used at each site and each membrane was used to filter 2 L of water. The filtered membranes were then placed in sterile petri dishes and stored at -80 °C until DNA extraction.
| 研究範圍 | This is a one-time sampling event. Water samples were collected from four sites along the Houdong Riverine zonation: the upstream waterfall (sample name: WF), river (FR), estuary (ES), and river mouth (RM). |
|---|
方法步驟描述:
- Wet lab process description: pending.
- Dry lab process description: pending.
- Lowest taxon level-annotation of each OTU was extracted to perform a secondary species mapping to GBIF Backbone using the rgbif package (Chamberlain et al., 2023; version 3.7.7) in R (R Core Team, 2022; version 4.2.2).
- Open data and code: We converted the occurrence data into Darwin Core Archive standard and validated data in both event and occurrence data sheets using the Data Validator developed by GBIF (Global Biodiversity Information Facility, 2017). We then published the dataset containing one event core and four extensions: occurrence, DNA derived data, extended measurement or facts, and resource relationship using The Integrated Publishing Toolkit (IPT) of GBIF installed under the Taiwan Biodiversity Information Facility (TaiBIF). DNA sequence data was submitted to European Nucleotide Archive under project accession PRJEB60905. All source codes used in the project can be found in the project GitHub repository (tbc link).
引用文獻
- European Nucleotide Archive EMBL-EBI Project. https://www.ebi.ac.uk/ena/browser/view/PRJEB60905
- Chamberlain S, Barve V, Mcglinn D, Oldoni D, Desmet P, Geffert L, Ram K (2023). rgbif: Interface to the Global Biodiversity Information Facility API. R package version 3.7.7. https://CRAN.R-project.org/package=rgbif
- R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/
額外的詮釋資料
| 替代的識別碼 | 2615342d-7349-4e75-ae34-cda6cb403e2e |
|---|---|
| https://ipt.taibif.tw/resource?r=houdongkeng_water_edna |