Supporting data for Petit-Marty et al. 2025. Genomic patterns and levels of genetic diversity reveal recent declines in the effective size of European hake populations. ICES JMS.

Analysed datasets supporting the results of Petit-Marty et al. 2025. Genomic patterns and levels of genetic diversity reveal recent declines in the effective size of European hake populations. ICES JMS. Analysed samples file lists: all_hake.filelist all_hake_nokin.filelist (used in Admixture and PCA analyses) Variant call files (VCF) for all individuals of the three analysed populations of European hake: File hake_pops_combined_nomiss.vcf: SNP calling was performed with no missing data, --minDP 10, --minQ 20 and minimun MAF for each population. Then, population's vcfs were combined. File all_pop_calls_unfiltered.vcf.gz : unfiltered SNP calls. Genetic diversity anallysis .sfs files: SFS each population (first column correspond to invariant sites. SFS is folded) .saf files : site allele frequency .theta files: genetic diversity estimates Admixture analysis: Admix_3pophake_nokin_nomiss.mafs.gz Admix_3pophake_nokin_nomiss.beagle.gz PCA: PCA_3pop_hake_nokin_nomiss.geno.gz PCA_3pop_hake_nokin_nomiss.mafs.gz The reference genome for these dataset can be found at https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_964660975.1/ Raw reads data have been deposited at NCBI SRA databse with ID PRJNA1329964 contact: [e-mail]