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
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.