Data from: Genome analysis reveals three distinct lineages of the cosmopolitan white shark

• Main Authors: Wagner, Isabel, Noble, Leslie, Jones, Catherine, Hoarau, Galice
• Format: Other/Unknown Material
• Language: unknown
• Published: Zenodo 2024
• Subjects: SNP; Carcharodon carcharias; population genomics; North Atlantic
• Online Access: https://doi.org/10.5281/zenodo.10992253

The white shark ( Carcharodon carcharias ) (Linnaeus, 1758), an iconic apex predator occurring in all oceans, is classified as Vulnerable globally with global abundance having dropped to 63% of 1970s estimates, and Critically Endangered in Europe. Identification of Evolutionary Significant Units and their management are crucial for conservation, especially as the white shark is facing various but often region-specific anthropogenic threats. Here, combining target gene capture sequencing (89 individuals, 4,000 SNPs) and whole genome re-sequencing (17 individuals, 391,000 SNPs), with worldwide sampling across most of the distributional range we identify three genetically distinct allopatric lineages (North Atlantic, Indo-Pacific, North Pacific). Funding provided by: Nord University ROR ID: https://ror.org/030mwrt98 Award Number: Target capture was performed on all 89 prepared genomic libraries using a bait set designed on the white shark genome and transcriptome. The captured libraries were split into two pools, which were sequenced on 1/4 of an Illumina NovaSeq S4 2x150 bp flow cell each. Target gene capture sequencing data was trimmed as described in Wagner et al. 2024, except for base call quality thresholds set to a phred of 30, and no length filter being applied. Read mapping and cleaning, Single Nucleotide Polymorphisms SNPs calling and hard filtering was performed following a pipeline developed in Wagner et al 2024, and using the white shark reference genome NCBI accession number GCF_017639515.1