Connections across open water: A bi-organelle, genomics-scale assessment of Atlantic-wide population dynamics in a pelagic, endangered apex predator shark (Isurus oxyrinchus)

Large-bodied pelagic sharks are key regulators of oceanic ecosystem stability, but highly impacted by severe overfishing. One such species, the shortfin mako shark (Isurus oxyrinchus), a globally widespread, highly migratory predator, has undergone dramatic population reductions and is now Endangered (IUCN Red List), with Atlantic Ocean mako sharks in particular assessed by fishery managers as overfished and in need of urgent, improved management attention. Genomic-scale population assessments for this apex predator species have not been previously available to inform management planning, thus we investigated the population genetics of mako sharks across the Atlantic using a bi-organelle genomics approach. Complete mitochondrial genome (mitogenome) sequences and genome-wide SNPs from sharks distributed across the Atlantic revealed contrasting patterns of population structure across marker types. Consistent with this species’ long-distance migratory capabilities, SNPs showed high connect..., Double-digest RADseq library preparation was performed per Peterson et al.’s (2012) protocol using the restriction enzymes SphI and MluC1 and raw sequence fastq reads were generated on an Illumina HiSeq 4000. This dataset contains raw sequence reads and associated individual barcode files., , # Data from: Connections across open water: A bi-organelle, genomics-scale assessment of Atlantic-wide population dynamics in a pelagic, endangered apex predator shark (Isurus oxyrinchus)

[https://doi.org/10.5061/dryad.2280gb63f](https://doi.org/10.5061/dryad.2280gb63f)

## Description of the data and file structure

Shortfin mako shark (*Isurus oxyrinchus*) SNP data was generated according to Peterson et al.’s (2012) double-digest RADseq protocol using restriction enzymes SphI and MluC1. Raw sequence reads of ddRADseq libraries were generated across three lanes of an Illumina HiSeq 4000.

### Files and variables

Raw sequence reads of ddRADseq generated from three lanes of of an Illumina HiSeq4000.

Raw sequence reads from each lane (i.e., mako01, mako02, and mako03) have been split into six separate .gz files (i.e., RAD-1, RAD-2 ... RAD-6), each containing raw fastq reads for eight sharks.

Each fastq.gz file has an associated key/barcode text file with shark ID and its associated ba...