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)
Data files
Jan 10, 2025 version files 99.77 GB
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mako01_barcode_RAD-1.txt
103 B
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mako01_barcode_RAD-2.txt
103 B
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mako01_barcode_RAD-3.txt
103 B
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mako01_barcode_RAD-4.txt
103 B
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mako01_barcode_RAD-5.txt
103 B
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mako01_barcode_RAD-6.txt
103 B
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mako01-RAD-1_R1.fastq.gz
5.47 GB
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mako01-RAD-2_R1.fastq.gz
6.92 GB
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mako01-RAD-3_R1.fastq.gz
4.74 GB
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mako01-RAD-4_R1.fastq.gz
4.71 GB
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mako01-RAD-5_R1.fastq.gz
5.21 GB
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mako01-RAD-6_R1.fastq.gz
6.75 GB
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mako02_barcode_RAD-1.txt
104 B
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mako02_barcode_RAD-2.txt
104 B
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mako02_barcode_RAD-3.txt
112 B
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mako02_barcode_RAD-4.txt
106 B
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mako02_barcode_RAD-5.txt
104 B
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mako02_barcode_RAD-6.txt
104 B
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mako02-RAD-1_R1.fastq.gz
7.22 GB
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mako02-RAD-2_R1.fastq.gz
7.74 GB
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mako02-RAD-3_R1.fastq.gz
2.79 GB
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mako02-RAD-4_R1.fastq.gz
6.31 GB
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mako02-RAD-5_R1.fastq.gz
6.47 GB
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mako02-RAD-6_R1.fastq.gz
2.01 GB
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mako03_barcode_RAD-1.txt
112 B
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mako03_barcode_RAD-2.txt
104 B
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mako03_barcode_RAD-3.txt
104 B
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mako03_barcode_RAD-4.txt
104 B
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mako03_barcode_RAD-5.txt
104 B
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mako03_barcode_RAD-6.txt
104 B
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mako03-RAD-1_R1.fastq.gz
8.39 GB
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mako03-RAD-2_R1.fastq.gz
6.82 GB
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mako03-RAD-3_R1.fastq.gz
5.66 GB
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mako03-RAD-4_R1.fastq.gz
2.78 GB
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mako03-RAD-5_R1.fastq.gz
6.67 GB
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mako03-RAD-6_R1.fastq.gz
3.11 GB
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README.md
2.80 KB
Abstract
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.
README: 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
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.
Methods
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.