DOI: 10.5061/dryad.9zw3r22mn
title: Original FASTQ files of: Global genetic diversity and historical demography of the Bull Shark

description: 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
 were performed to determine the detectability of recent bottleneck under
 the estimated historical trend for datasets of this size. Results Three
 genetic clusters corresponding to the IPA, WTA and EPA regions were
 identified, agreeing with previous studies. The IPA presented the highest
 genetic diversity and was consistently identified as the oldest. No
 significant within-cluster structuring was detected. Ne increased
 globally, with an earlier onset in the IPA, during the last glacial
 period. Coalescent simulations showed that weak and recent bottlenecks
 could not be detected with our dataset, while old and/or strong
 bottlenecks would erase the observed ancestral expansion. Main conclusions
 This study further confirms the role of marine biogeographic breaks in
 shaping the genetic history of large mobile marine predator. Ne Historical
 increases of Ne are potentially linked to extended coastal habitat
 availability. The limited within-cluster population structuring suggests
 that Ne can be monitored over ocean basins. Due to insufficient amount of
 available genetic data, it cannot be concluded whether overfishing is
 impacting Bull Shark genetic diversity, calling for whole genome
 sequencing.
description: <strong>Sample collection and DNA
 extraction</strong> A subsample of the dataset of
 Devloo-Delva et al. (2023) was used for this study, representing 475
 <em>C. leucas</em> sampled between 1985 and 2019 from 18
 locations covering its distribution (except for West Africa; Supplementary
 Material 1)<em>.</em> 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.
 <strong>SNP selection for bait
 design</strong> 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 DArTseq<sup>TM</sup>
 approach (Cruz et al., 2013; Feutry et al., 2017, 2020, Supplementary
 material 1). From this dataset, 3,400 loci of 70 bp were randomly selected
 for DNA-capture bait development. The
 DArTcap<sup>TM</sup> enriched libraries
 were sequenced on a Illumina HiSeq 2500.
description: # 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, F.,
 Burridge, C P., Kyne, P M., Brunnschweiler, J M., Chapman, D D., Charvet,
 P., Chen, X., Cliff, G., Daly, R., Drymon, J M., Espinoza, M., Fernando,
 D., Barcia, L G., Glaus, K., González-Garza, B I., Grant, M I.,
 Gunasekera, R M., Hernandez, S., Hyodo, S. … Feutry, P. (2023). From
 rivers to ocean basins: The role of ocean barriers and philopatry in the
 genetic structuring of a cosmopolitan coastal predator. Ecology and
 Evolution, 13, e9837. ( ) The
 parameters used to select this subset are described in the Material and
 Methods section of *Global genetic diversity and historical demography of
 the Bull Shark*