DOI: 10.5061/dryad.j3tx95xnq
title: Data from: Evidence for gene flow from the Gulf of Mexico to the Atlantic Ocean in bonnethead sharks (Sphyrna tiburo)

description: 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 connectivity between
 Tampa Bay on the Gulf Coast of Florida and Biscayne Bay on the Atlantic
 coast of Florida. While standard analyses of genetic structure revealed
 slight but significant differentiation between Tampa Bay and Biscayne Bay
 populations, demographic history inference based on the site frequency
 spectrum favored a model without divergence. However, we also estimate
 that if population divergence occurred, it would have been recent (between
 1,500 - 4,500 years ago), with continuous unidirectional gene flow from
 Tampa Bay to Biscayne Bay. Our findings support the hypothesis that
 bonnetheads can migrate over relatively large distances (&gt;300
 miles) to find mates. Together, these results provide optimism that under
 proper management, a small-bodied globally Endangered shark can undergo
 long migrations to sustain genetic diversity.
description: # 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 samples),
 `Bonnet2.ibsMat` (Identity-by-State genetic distance matrix), four `*qopt
 `files (for admixture scenarios k=1-4), and `Bonnetsmeta.txt `(containing
 site and morphological information for each sample). Variables in
 `Bonnets_meta.txt` include:  TubeID: Extra tube labels during sample
 collection Maturity_fieldob: Four maturity designations (YOY, immature,
 subadult, mature) estimated during sample collection Sex: Male/ Female
 Location: Site names during sample collection PCL (cm): Precaudal length
 FL (cm): Fork length TL (cm): Stretched total length Girth (cm) Eye2eye
 (cm) Bluge_slope (cm) Mouth_width (cm) Maturity (cm): Mature, immature
 only ## Code/Software Reads are deposited in the SRA (Bioproject:
 PRJNA1082259). We used the Texas Advanced Computing Center (TACC) for all
 bioinformatic analyses. All figures were produced in R.