Data for <b>Genomic baseline reveals vulnerable genetically depauperate pocket within highly structured Norwegian kelp forests</b>

To create this file, we processed ddRAD-seq reads using a reference-based approach. After proceeding with the demultiplexing using process_radtags, we merged replicates by individual and filtered the reads with the FASTX toolkit to retain sequences with >99% of bases scoring a Phred quality ≥20.

We aligned the filtered reads to the L. digitata reference genome (Phaeoexplorer: LdigPH10-18mv Male, n.d.), called SNPs with gstacks, and extracted genotypes using populations (-p 1 -r 10) before SNP filtering (VCFtools), yielding 1.64 million SNPs from 208 individuals. To improve data quality, we removed SNPs (RStudio) with anomalously high read depth (>2× mean), low read depth (<8), minor allele frequency <0.1%, or significant deviations from Hardy-Weinberg equilibrium (HWE, p < 1 × 10⁻¹⁰, VCFtools::--hwe).