Original FASTQ files of: Global genetic diversity and historical demography of the Bull Shark

Aim
Biogeographic boundaries and genetic structuring have important effects on the inferences and interpretation of effective population size (Ne) temporal variations, a key genetics parameter. We reconstructed the historical demography and divergence history of a vulnerable coastal high-trophic shark using population genomics and assessed our ability to detect recent bottlenecks events.
Location
Western and Central Indo-Pacific (IPA), Western Tropical Atlantic (WTA), Eastern Tropical Pacific (EPA)
Taxon
Carcharhinus leucas (Müller & Henle, 1839)
Methods
A DArTcapTM approach was used to sequence 475 samples and assess global genetic structuring. Three demographic models were tested on each population, using an ABC-RF framework coupled with coalescent simulations, to investigate within-cluster structure. Divergence times between clusters were computed, testing multiple scenarios, with fastsimcoal. Ne temporal variations were reconstructed with STAIRWAYPLOT. Coalescent simulations wer..., Sample collection and DNA extraction
A subsample of the dataset of Devloo-Delva et al. (2023) was used for this study, representing 475 C. leucas sampled between 1985 and 2019 from 18 locations covering its distribution (except for West Africa; Supplementary Material 1). DNA was extracted with the Qiagen Blood and Tissue kit, following standard protocol (Qiagen Inc., Valencia, California, USA). After bait design and bioinformatic filtering (see following sections), the dataset comprised 16 sampling locations with at least five individuals (309 individuals; Fig. 1, Table 1) covering the WTA, IPA, and EPA. Sampling locations with mostly adults were preferentially selected to limit relatedness effects.
SNP selection for bait design
The approach used for bait design is described in Devloo-Delva et al. (2023). Briefly, a subset of 219 sample libraries were genotyped using the DArTseqTM approach (Cruz et al., 2013; Feutry et al., 2017, 2020, Supplementary material 1). From this dataset, 3,400..., , # Original FASTQ files of \"Global genetic diversity and historical demography of the Bull Shark\"

Publication:

dataset DOI:10.5061/dryad.9zw3r22mn

The original 512 FASTQ files (475 individuals) and their metadata, including the final list of 309 individuals used to generate the results of this study, using DArTcap sequencing and based on the Dataset used in Devloo-Delva et al. 2023 ( )

## **## Description of the data and file structure**

There are 512 individual Bull Shark FastQ files, unfiltered and including technical replicates. These files have a unique ID, which allows identifying the samples' metadata in the provided Tab delimited text. The final dataset used in the study (309 individuals) is also indicated in the metadata file, allowing to reproduce the results using STACKS (Genotyping-by-Sequencing analysis software).

There are no abbreviations in the metadata file.

## **## Sharing/Access information**

This dataset is a subset of the dataset produced in :

Devloo-Delva...