DOI: 10.5061/dryad.8pk0p2nwh
title: Data from: Genome analysis reveals three distinct lineages of the cosmopolitan white shark

description: 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).
description: 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
description: # Data from: Genome analysis reveals three distinct lineages of the
 cosmopolitan white shark
 [https://doi.org/10.5061/dryad.8pk0p2nwh](https://doi.org/10.5061/dryad.8pk0p2nwh) This folder contains the data, computer code and document files for the article: Wagner et al 2024. Seeing the bigger picture: Genome analysis reveals three distinct lineages of the cosmopolitan white shark. Current Biology Comments and requests should be addressed to Galice Hoarau: [galice.g.hoarau@nord.no](mailto:galice.g.hoarau@nord.no). All material is free of use, but I would appreciate being told, and this dataset and the matching paper cited if appropriate. ## Description of the data and file structure The file named Sample_info_complete.xlsx contains the information relative to the samples used in the publication. | Sample ID: unique identifier, also used in the VCF file | | :--------------------------------------------------------------------------------------------------- | | Sample Group: geographic region the individual was sampled | | Sampling Location: The location that the specimen was obtained from | |  Sex:  M(ale), F(emale) U(nknown) | | Total Length in cm, U(nknown) | | DNA repaired: indicates if the DNA was repaired prior to library preparation (see Wagner et al 2024) | | WGS total read number: total number of read from Illumina whole genome sequencing  | | TGC total read:  total number of read from Illumina target gene capture sequencing  | The file named TGC_GWS_snps.vcf contains the SNPs genotypes (target gene capture) for all the individuals describes in  Sample_info_complete.xlsx using the same Sample ID The file named  ANGSD_LD.py is a Python script used for thinning the data as described in Wagner et al 2024 ## Code/Software The file named  ANGSD_LD.py is a Python script used for thinning the data