DOI: 10.5061/dryad.2280gb63f
title: 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)

description: 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 connectivity and Atlantic panmixia overall. In contrast, there
 was matrilineal population genetic structure across Northern and Southern
 Hemispheres, suggesting at least large regional-scale female philopatry.
 Linkage disequilibrium network analysis indicated that makos possess a
 chromosomal inversion that occurs Atlantic wide, a genome feature that may
 be informative for evolutionary investigations concerning adaptations and
 the global history of this iconic species. Mitogenome diversity in
 Atlantic makos was high compared to other elasmobranchs assessed at the
 mitogenome level, and nuclear diversity was high compared to the two
 other, highly migratory pelagic shark species assessed with SNPs. These
 results support management efforts for shortfin makos on at least Northern
 versus Southern Hemisphere scales to preserve their matrilineal genetic
 distinctiveness. The overall comparative genetic diversity findings
 provide a baseline for future comparative assessments and monitoring of
 genetic diversity, as called for by the United Nations Convention on
 Biological Diversity, and cautious optimism regarding the health and
 recovery potential of Atlantic shortfin makos if further population
 declines can be halted.
description: 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.
description: # 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 barcode identfier (i.e., mako01_barcode_RAD-1.txt). List of files, file size, and file counts: Lane 1 Raw Sequence Reads: mako01-RAD-1_R1.fastq.gz, 5.47 GB, 1 file mako01-RAD-2_R1.fastq.gz, 6.92 GB, 1 file mako01-RAD-3_R1.fastq.gz, 4.74 GB, 1 file mako01-RAD-4_R1.fastq.gz, 4.71 GB, 1 file mako01-RAD-5_R1.fastq.gz, 5.21 GB, 1 file mako01-RAD-6_R1.fastq.gz, 6.75 GB, 1 file Lane 2 Raw Sequence Reads: mako02-RAD-1_R1.fastq.gz, 7.22 GB, 1 file mako02-RAD-2_R1.fastq.gz, 7.74 GB, 1 file mako02-RAD-3_R1.fastq.gz, 2.79 GB, 1 file mako02-RAD-4_R1.fastq.gz, 6.31 GB, 1 file mako02-RAD-5_R1.fastq.gz, 6.47 GB, 1 file mako02-RAD-6_R1.fastq.gz, 2.01 GB, 1 file Lane 3 Raw Sequence Reads: mako03-RAD-1_R1.fastq.gz, 8.93 GB, 1 file mako03-RAD-2_R1.fastq.gz, 6.82 GB, 1 file mako03-RAD-3_R1.fastq.gz, 5.66 GB, 1 file mako03-RAD-4_R1.fastq.gz, 2.78 GB, 1 file mako03-RAD-5_R1.fastq.gz, 6.67 GB, 1 file mako03-RAD-6_R1.fastq.gz, 3.11 GB, 1 file Lane 1 barcode files: mako01_barcode_RAD-1.txt, 103 B, 1 file mako01_barcode_RAD-2.txt, 103 B, 1 file mako01_barcode_RAD-3.txt, 103 B, 1 file mako01_barcode_RAD-4.txt, 103 B, 1 file mako01_barcode_RAD-5.txt, 103 B, 1 file mako01_barcode_RAD-6.txt, 103 B, 1 file Lane 2 barcode files: mako02_barcode_RAD-1.txt, 104 B, 1 file mako02_barcode_RAD-2.txt, 104 B, 1 file mako02_barcode_RAD-3.txt, 112 B, 1 file mako02_barcode_RAD-4.txt, 106 B, 1 file mako02_barcode_RAD-5.txt, 104 B, 1 file mako02_barcode_RAD-6.txt, 104 B, 1 file Lane 3 barcode files: mako03_barcode_RAD-1.txt, 112 B, 1 file mako03_barcode_RAD-2.txt, 104 B, 1 file mako03_barcode_RAD-3.txt, 104 B, 1 file mako03_barcode_RAD-4.txt, 104 B, 1 file mako03_barcode_RAD-5.txt, 104 B, 1 file mako03_barcode_RAD-6.txt, 104 B, 1 file ## Code/software No special software needed to read files.