Overview
The edna/ dataset contains all environmental DNA (eDNA) data collected during Pristine Seas expeditions. eDNA sampling provides a non-invasive method to assess marine biodiversity by detecting genetic material shed by organisms into the water column.
The eDNA protocol involves collecting water samples at standardized depths and locations, filtering them to capture genetic material, and preserving the filters for subsequent laboratory analysis. This approach enables detection of species that may be difficult to observe through traditional visual methods, including cryptic, rare, or elusive taxa.
The dataset structure captures the hierarchical nature of eDNA sampling:
- Sites: Deployment locations where eDNA collection occurred
- Stations: Depth-stratified sampling units within each site
- Samples: Individual water samples with specific collection and processing metadata
- Detections: Species identifications from laboratory analysis (future implementation)
edna/
├── sites # Deployment-level metadata for eDNA collection locations
├── stations # Depth-stratified sampling metadata
├── samples # Individual water sample collection and processing data
└── detections # Species detections from laboratory analysis (future)
Tables
Sites (edna.sites)
The edna.sites table contains one row per environmental DNA (eDNA) sampling site. Each site represents a distinct point in space and time where eDNA collection was deployed, serving as the primary spatial unit for eDNA fieldwork. Within a site, multiple water samples may be collected across different depth strata, recorded in the corresponding edna.stations table.
This table stores site-level metadata for all eDNA collection deployments, typically coordinated with other survey methods like UVS or BRUVS. It follows the core site schema shared across all methods and adds eDNA-specific fields including target taxa, coordination with paired survey methods through paired_site_id, and site documentation. The table captures spatial metadata, sampling platform, habitat descriptors, and effort summaries.
target — Indicates the primary taxonomic focus for laboratory analysis:
fish — General fish diversity assessmentsharks — Specialized primers for elasmobranch detection
all_taxa — Broad taxonomic coverage using universal primersspecific_taxa — Targeted detection of particular species or groups
paired_site_id — Links eDNA sites to paired visual underwater surveys or BRUVS deployments.
Stations (edna.stations)
This table contains metadata for depth-stratified eDNA sampling stations. Each row represents a discrete sampling unit within a site, corresponding to a specific depth stratum where multiple replicate samples were collected.
Stations follow the standard Pristine Seas depth stratification and include summary metrics about collection effort. Key spatial and site metadata are denormalized here to minimize joins for common analyses.
Samples (edna.samples)
This table contains detailed metadata for individual water samples. Each row represents a single replicate sample with specific collection parameters, processing details, and preservation information. Key station and site metadata are denormalized to enable efficient querying without multiple joins.