Data accompanying: Large-scale biogeographic structuring of Pacific abyssal communities revealed by eDNA metabarcoding

This repository contains the processed data, metadata, analysis code, figures, and supplementary materials associated with the study “Large-scale biogeographic structuring of Pacific abyssal communities revealed by eDNA metabarcoding”, which investigates biodiversity and biogeographic structuring across >5,700 km of the Pacific abyssal plain using environmental DNA (eDNA) metabarcoding. The study analysed 252 eDNA samples collected at depths of 4,289–5,666 m between Mexico, Hawai‘i and Tahitī using three metabarcoding assays: COI Leray, MiFish-U, and 16S Fish. Analyses examined basin- and site-scale patterns in taxonomic diversity and community composition, environmental and spatial associations, distance-decay and taxonomic turnover, and differences among near-bottom Niskin and passive eDNA sampling approaches. The zipped analysis archive contains the files required to support and reproduce the analyses presented in the manuscript, including: processed metabarcoding data and outputs; sample and environmental metadata; taxonomic curation data and outputs; R code used for statistical analyses and figure generation; manuscript figures and associated outputs; map and spatial data; and supplementary material and supporting analysis outputs. Sample metadata are also provided separately to facilitate access without downloading the complete analysis archive. Raw sequencing reads are deposited in the European Nucleotide Archive (ENA) under project accession PRJEB123800. Outputs generated by the OceanOmics metabarcoding bioinformatics pipeline are additionally available through the OceanOmics public S3 data repository. The directory structure within the zipped archive has been retained to preserve the relative file paths used by the accompanying R analysis project and Quarto workflow. This work was supported by the Minderoo Foundation and the Minderoo OceanOmics Centre at The University of Western Australia. This research was also funded by the marine research organisation Inkfish LLC as part of its Open Ocean Program. Computational resources were provided by the Pawsey Supercomputing Research Centre with funding from the Australian Government and the Government of Western Australia.