Environmental DNA reveals diverse and depth-stratified biodiversity in East Indian Ocean submarine canyons

This data accompanies the manuscript of the same title (Nester et al., 2026). A descriptor of each file is provided in DataFileDescriptor.xlsx. As Zenodo does not allow folder updates, a suggested folder structure is also provided. ROV imagery and annotations are available on Squidle+ through campaign FK200308 (https://squidle.org/geodata/explore#map). Cruise data, bathymetry, and related expedition information are accessible via the Schmidt Ocean Institute (https://schmidtocean.org/cruise/illuminating-biodiversity-of-ningaloo-canyons/#data) and AusSeabed (https://www.ausseabed.gov.au/data). All data generated and R scripts created in this study have been deposited in this Zenodo repository (10.5281/zenodo.18581057). This includes sampling information, raw sequencing data, morphology data, ZOTU tables for both metabarcoding assays, and results of statistical analyses. Custom DNA reference sequences are available on NCBI (see Supplementary Table 3 for GenBank accession numbers), but are also provided in this repository.