DOI: 10.5061/dryad.gqnk98sv8
title: Data from: 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

description: 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, 237 orders, and 402 families. The highest family richness was
 found for the phyla Arthropoda, Bacillariophyta and Chordata. Overall,
 family richness was similar between depths but decreased during summer, a
 pattern consistent at both locations. Our results indicate that the
 structure (composition) of the mesophotic communities varied predominantly
 with seasons. We analyzed further the better-resolved fish assemblage and
 compared eDNA with other visual methods at the same locations and depths.
 We recovered eDNA from nineteen genera of fish, six of these have also
 been observed on towed underwater videos, while thirteen were unique to
 eDNA. We discuss the potential drivers of seasonal differences in
 community composition and richness. Our results suggest that eDNA can
 provide valuable insights for monitoring TMRE communities but highlight
 the necessity of completing reference DNA databases available for this
 region.
description: # 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 pipeline. Each
 Sheet corresponds to the "taxonomy_detailed.txt" files produced
 by Anacapa. For each ASV the following information is provided: DNA
 sequence, read abundance for each sample, blast alignment statistics,
 assigned taxonomy, taxonomy confidence (BCLA), and accession numbers of
 blast matches. ## Description of the data and file structure Data files
 are standard fastq sequence data files obtained using Illumina Miseq
 sequencing technology. Files were demultiplexed using Geneious Prime
 2022.0.2.