說明
Data were collected during a dedicated campaign to study eDNA in the French Caribbean archipelago of Guadeloupe, organized and financed by the UMR ISYEB and the Labex DRIIHM, and beneficiating of a collaboration with the NGO OMMAG (Observatoire des Mammifères Marins de l’Archipel Guadeloupéen - Guadeloupe Archipelago Marine Mammal Observatory) for at sea campaigns.
The project consisted in taking and analysing eDNA samples using, on consecutive days, a same protocol on a same transect along the west coast of Guadeloupe. Twelve samples were taken. Two sampling phases were carried out: one in 2021 over four consecutive days, the other in 2022 over two consecutive days. eDNAs contained in the samples were analysed by metabarcoding using vertebrate–specific primers (Taberlet et al. 2018). The resulting dataset consisted in lists of vertebrate taxa identified from analysed MOTU (Molecular Taxonomic Unit - a grouping of sequences based on their molecular similarity) in the different samples. The taxonomic assignments were made at the most precise taxonomic rank possible.
The project resulted in a local taxonomic inventory of marine vertebrates based on eDNA. Comparison between samples provided an overview of the short and middle terms temporal variations in taxonomic composition at a single sampling point, as captured by our eDNA sampling and analysis protocols.
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 200 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。:
Haderlé R, Ung V, Jung J (2024). eDNA-based survey of the marine vertebrate biodiversity off the west coast of Guadeloupe (French West Indies). Version 1.7. MNHN - Museum national d'Histoire naturelle. Occurrence dataset. https://ipt.gbif.fr/resource?r=edna_marine_vertebrates_guadeloupe&v=1.7
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 MNHN - Museum national d'Histoire naturelle。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.
GBIF 註冊
此資源尚未向GBIF註冊
關鍵字
Occurrence; Environmental DNA; Vertebrates; West Indies; 12S Mitochondrial Ribosomal RNA; Metabarcoding
聯絡資訊
- 出處
- Research engineer
- 出處
- Research Director
地理涵蓋範圍
The Guadeloupe islands are located in the Caribbean Sea, at the heart of the Agoa sanctuary, a large marine protected area (over 143,000 km²) corresponding to the entire French Exclusive Economic Zone of the French West Indies and dedicated to the protection and conservation of marine mammals. The sampling area is located on the west coast of Guadeloupe island on the Caribbean Seaside, the leeward coast, off the commune of Bouillante in Basse Terre. The sampling transect was approximately 5 km long. This transect is located on a very marked bathymetric drop-off (over 1000 m deep) and links two GPS points with coordinates (16.125°, -61.849°) and (16.081°, -61.833°). This specific zone was selected because of the drop-off and numerous sightings of cetaceans, with a particular emphasis on Physeter macrocephalus, as regularly reported by whale watchers in this area (Coché et al. 2021).
| 界定座標範圍 | 緯度南界 經度西界 [16.103, -61.841], 緯度北界 經度東界 [16.103, -61.841] |
|---|
分類群涵蓋範圍
N/A
| Kingdom | Animalia |
|---|---|
| Phylum | Chordata |
| Class | Mammalia, Actinopterygii |
| Order | Stomiiformes, Beloniformes, Cetacea, Perciformes, Acanthuriformes, Scombriformes, Carangiformes, Aulopiformes, Acropomatiformes, Myctophiformes, Trachiniformes |
| Family | Chiasmodontidae, Bramidae, Pomacanthidae, Stomiidae, Scombridae, Coryphaenidae, Exocoetidae, Carangidae, Myctophidae, Istiophoridae, Labridae, Chaetodontidae, Bathyclupeidae, Nomeidae, Scopelarchidae, Delphinidae, Lutjanidae, Belonidae, Hemiramphidae, Neoscopelidae, Pomacentridae, Evermannellidae, Gempylidae |
時間涵蓋範圍
| 起始日期 / 結束日期 | 2021-06-06 / 2022-02-11 |
|---|
計畫資料
The project consisted in taking and analysing eDNA samples using, on consecutive days, a same protocol on a same transect along the west coast of Guadeloupe. Twelve samples were taken. Two sampling phases were carried out: one in 2021 over four consecutive days, the other in 2022 over two consecutive days. eDNAs contained in the samples were analysed by metabarcoding using vertebrate–specific primers (Taberlet et al. 2018).
| 計畫名稱 | eDNA-based survey of the marine vertebrate biodiversity off the west coast of Guadeloupe (French West Indies) |
|---|---|
| 經費來源 | Data were collected during a dedicated campaign to study eDNA in the French Caribbean archipelago of Guadeloupe, organized and financed by the UMR ISYEB and the Labex DRIIHM, and beneficiating of a collaboration with the NGO OMMAG (Observatoire des Mammifères Marins de l’Archipel Guadeloupéen - Guadeloupe Archipelago Marine Mammal Observatory) for at sea campaigns. |
| 研究區域描述 | The Guadeloupe islands are located in the Caribbean Sea, at the heart of the Agoa sanctuary, a large marine protected area (over 143,000 km²) corresponding to the entire French Exclusive Economic Zone of the French West Indies and dedicated to the protection and conservation of marine mammals. The sampling area is located on the west coast of Guadeloupe island on the Caribbean Seaside, the leeward coast, off the commune of Bouillante in Basse Terre. The sampling transect was approximately 5 km long. This transect is located on a very marked bathymetric drop-off (over 1000 m deep) and links two GPS points with coordinates (16.125°, -61.849°) and (16.081°, -61.833°). This specific zone was selected because of the drop-off and numerous sightings of cetaceans, with a particular emphasis on Physeter macrocephalus, as regularly reported by whale watchers in this area (Coché et al. 2021). |
取樣方法
All samples were collected from a motorised rigid inflatable boat during 30 minutes at a 5-knot speed. For all samples, the boat followed a same transect defined on top of a marked bathymetric drop-off parallel to the coast. During each transect, two samples of seawater were collected in front of the boat, one from each side of the boat, just below the sea surface. For each sample, 30L of sea water were continuously filtered through a VigiDNA 0.2 μM filtration capsule (SPYGEN, France) using an Athena peristaltic pump (Proactive, Hamilton, NJ, USA), as described in Dalongeville et al. (2022). Right after the completion of the procedure, each capsule was filled with 80 mL of CL1 DNA preservation buffer (SPYGEN) and stored at room temperature until DNA extraction.
| 研究範圍 | This transect is located on a very marked bathymetric drop-off (over 1000 m deep) and links two GPS points with coordinates (16.125°, -61.849°) and (16.081°, -61.833°). Two sampling phases were carried out: one in 2021 on four consecutive days (from 06/06/2021 to 06/09/2021), the other in 2022 on two consecutive days (02/10/2022 and 02/11/2022). |
|---|---|
| 品質控管 | Data were checked for errors: 10% of MOTUs were randomly selected and checked by two people: taxonomic assignment was repeated and the number of reads per sample was confirmed. No errors were detected. |
方法步驟描述:
- DNA extraction and amplification were performed by a dedicated DNA laboratory (SPYGEN, www.spygen.com). PCR amplification was performed using a universal vertebrate 12S mitochondrial rDNA primer pair Vert01 (TAGAACAGGCTCCTCTAG and TTAGATACCCCACTATGC, Taberlet et al. 2018). The amplicons were then sequenced using an Illumina MiSeq sequencer (Illumina, San Diego, CA, USA). The resulting sequence datasets (read sets) were analysed using the OBITools package (Boyer et al. 2015) for taxonomic assignment. Each MOTU, representing a grouping of sequences based on their molecular similarity, was associated with a number of reads per sample. MOTUs were named using the following nomenclature: Gua_Boui_V_Year_n°MOTU; with Gua for Guadeloupe, Boui, a 4-letter code for "Bouillante" (commune located on the shore the closest to the transect), V for the primer used, in this case specific to vertebrates, the sampling year (2021 or 2022), and a number corresponding to the order of appearance of the MOTU in the overall list. The taxonomic assignment of each MOTU was meticulously checked by hand. To compare the taxonomic resolution and the detection powers of different primers, two samples SPY210556 and SPY204197, respectively taken the 06/06/2021 and the 06/09/2021, were also analysed with a pair of primers specific to teleosts, Tele01 (ACACCGCCCGTCACTCT, CTTCCGGTACTACCATG, Valentini et al. 2016). Similarly, the 2021 samples (SPY204198, SPY204172, SPY210555 and SPY204197) were also analysed with a pair of Mamm01 mammal-specific primers (CCGCCCGTCACYCTCCT, GTAYRCTTACCWTGTTACGAC, Taberlet et al. 2018) and with a pair of cetacean-specific primers 175f-407r (CATACGATAAGTTAAAGCTCG, GATCATTACTAGCTACCCCC, Girardet & Jung. unpublished).
引用文獻
- Boyer, F., Mercier, C., Bonin, A., Le Bras, Y., Taberlet, P. and Coissac, E. (2016). obitools: a unix-inspired software package for DNA metabarcoding. Mol Ecol Resour 16, 176–182.
- Coché, L., Arnaud, E., Bouveret, L., David, R., Foulquier, E., Gandilhon, N., Jeannesson, E., Le Bras, Y., Lerigoleur, E., Lopez, P. J., et al. (2021). Kakila database: Towards a FAIR community approved database of cetacean presence in the waters of the Guadeloupe Archipelago, based on citizen science. Biodivers Data J 9, e69022.
- Dalongeville, A., Boulanger, E., Marques, V., Charbonnel, E., Hartmann, V., Santoni, M. C., Deter, J., Valentini, A., Lenfant, P., Boissery, P., et al. (2022). Benchmarking eleven biodiversity indicators based on environmental DNA surveys: More diverse functional traits and evolutionary lineages inside marine reserves. Journal of Applied Ecology59, 2803–2813.
- Taberlet, P., Bonin, A., Zinger, L. and Coissac, E. (2018). Environmental DNA: For Biodiversity Research and Monitoring. Oxford University Press.
- Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., Bellemain, E., Besnard, A., Coissac, E., Boyer, F., et al. (2016). Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology 25, 929–942.