Genome analysis reveals three distinct lineages of the cosmopolitan white shark

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).

Methods
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