Microbial and small zooplankton communities predict density of baleen whales in the southern California Current Ecosystem

Data repository for: Microbial and small zooplankton communities predict density of baleen whales in the southern California Current Ecosystem (Satterthwaite et al.). This record contains processed data and validation partitions needed to reproduce the analysis in the associated code repository (github.com/ruizt/marine-mammal-edna). Processed data (ncog16s.RData, ncog18sv4.RData, ncog18sv9.RData, density-estimates.RData, sightings.RData): Cleaned and normalized amplicon sequence variant (ASV) abundance tables for three eDNA markers (16S rRNA, 18S rRNA V4, 18S rRNA V9) and line-transect density estimates for three baleen whale species (blue, fin, humpback) across CalCOFI cruises in the southern California Current Ecosystem, 2014–2020. Raw amplicon data are not included but may be requested from the authors. Line transect input data (sample_table.Rds, region_table.Rds, obs_table.Rds): Effort and detection data used in the distance-sampling analysis of whale survey data (see supplementary line transect vignette in code repository). Validation partitions (_partitions.zip, _combined-partitions.zip): Leave-one-out and nested cross-validation partitions for the three eDNA markers, used in stability selection and nested validation steps of the analysis. These files are large (~5.5 GB total) and are not required to reproduce model fitting from stable sets; see the code repository README for details. Processed data workbook (data.xlsx): All processed data in tabular form, including ASV abundance tables with taxonomic annotations, sample metadata, and density and sighting records.