Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes, the Providencia island data set.
Between June 29 and July 5, 2018, we collected a total of 20 water samples from 10 stations around Providencia Island, with two filtration replicates per station. Providencia Island is located in the southwestern Caribbean Sea and forms part of the UNESCO Seaflower Biosphere Reserve in Colombia. This island, which belongs to the San Andrés, Providencia, and Santa Catalina Archipelago, is characterized by a complex barrier reef on a calcareous platform surrounding an extinct Miocene volcano. The high habitat diversity provides a range of substratum types and coral reefs, influencing the diversity, abundance, and distribution of coral reef fishes. Each station consisted of a transect of 2 km at an overall constant distance from the coast. We recorded the GPS coordinates at the start and end of the transect. We conducted eDNA sampling by using a filtration device composed of an Athena® peristaltic pump (Proactive Environmental Products LLC, Bradenton, Florida, USA; nominal flow of 1.0 L/min), a VigiDNA® 0.20 μM cross-flow filtration capsule (SPYGEN, le Bourget du Lac, France) and disposable sterile tubing for each filtration capsule. We performed two filtration replicates in parallel on each side of a boat, at each station, for 30 min corresponding to a volume of ~30 L of water filtered by each capsule. At the end of each filtration, the water inside the capsules was emptied, and we filled the capsules with 80 ml of CL1 Conservation buffer (SPYGEN, le Bourget du Lac, France) and stored at room temperature. We followed a strict contamination control protocol in both field and laboratory stages (Valentini et al., 2016). Each water sample processing included the use of disposable gloves and single-use filtration equipment to avoid any risk of contamination. Libraries were prepared with ligation using the MetaFast protocol (Fasteris).
Data content:
* rawdata/: contains the raw reads for each individual sample. One archive contains the paired-end reads specified by the _R1 or _R2 suffix as well as individually tagged PCR replicates (if available) together with an archive containing all extraction and PCR blank samples of the library. Reads have been demultiplexed using cutadapt but not trimmed, individual demultiplexing tags and primers remain present in the sequences.
* taxadata/: contains the table with all detected taxonomy for each sample after bioinformatic processing (see Polanco et al. 2020 for details; https://doi.org/10.1002/edn3.140) and associated field metadata.
* metadata/: contains two metadata files, one related to the data collected in the field for each filter, and the second related to the sequencing process in the lab (including the tag sequence, library name, and marker information for each sample)
