environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: towards a baseline for biodiversity monitoring of unexplored marine habitats

Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better-studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, ..., , , # Environmental DNA reveals temporal and depth variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: towards a baseline for biodiversity monitoring of unexplored marine habitats

The main data files are three compressed (zip) files containing 390 fastq paired files (R1 and R2). These correspond to the demultiplexed of water eDNA samples sequenced with three metabarcodes. Names of each file indicate the corresponding metabarcode.
The accompanying sheet \"metadata.csv\" contains information for each sample. This files contains a column with each fastq file name, and the following columns indicating the corresponding metabarcode for each sequence file, the type of sample (sample vs. control, and for control what kind of control), and for samples, the sampling site code informed in the main text.

One additional Excel file is provided (ASV_tables.xlsx). This file includes three sheets, each with all the ASVs recovered from sequence files using the Anacapa pipe...