Evidence for gene flow from the Gulf of Mexico to the Atlantic Ocean in bonnethead sharks (Sphyrna tiburo)

Gene flow is important for maintaining the genetic diversity required for adaptation to environmental disturbances, though gene flow may be limited by site fidelity in small coastal sharks. Bonnethead sharks (Sphyrna tiburo) - a small coastal hammerhead species - demonstrate site fidelity, as females are philopatric while males migrate to mediate gene flow. Consequently, bonnetheads demonstrate population divergence with distance and Atlantic populations are genetically distinct from those of the Gulf of Mexico. Indeed, Florida forms a vicariant zone between these two bodies of water for many marine species, including some sharks. However, while bonnetheads are expected to have limited dispersal, the extent and rate of bonnethead migration remains uncertain. Thus, we aimed to determine their dispersal capacity by evaluating connectivity between disparate populations from the Gulf of Mexico and Atlantic Ocean. Using 10,733 SNPs derived from 2bRAD sequences, we evaluated genetic connectiv..., , , # Genomic evidence for bonnethead shark (Sphyrna tiburo) migration from the Gulf of Mexico to the Atlantic Ocean

[https://doi.org/10.1002/ece3.70334](https://doi.org/10.1002/ece3.70334)

## Description of the data and file structure

`Bonnethead_2bRAD.sh` contains instructions to trim and filter reads, genotype samples, run GADMA for demographic inference, and calculate Fst and inbreeding coefficients. Data input for these scripts include: `d2.sfs` (site frequency spectrum for GADMA) and \"`sfs`\" (folder): contains 100 bootstrapped sfs for custom model selection procedure. All genetic data can be accessed from the Sequence Read Archive under Bioproject: PRJNA1082259 (Accession nos.: SAMN40202348- SAMN40202454).

Use `Bonnethead_popstructure.R` to reproduce figures and results from the manuscript- including dendrograms and PCoA of IBS and relatedness genetic distances, Admixture barplots, and RDA biplots. Data input for these scripts include: `bams.qc` (list of bam files or individual sa...