RADseq data for Atlantic Halibut in the Northwest Atlantic
Data files
Feb 19, 2021 version files 5.62 GB
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Halibut_finalgenome_mindp15_24chrom_ming90_HWE_noWF_allENV.fam
23.90 KB
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Halibut_finalgenome_mindp15_24chrom_ming90_HWE_noWF_allENV.map
2.22 MB
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Halibut_finalgenome_mindp15_24chrom_ming90_HWE_noWF_allENV.ped
252.65 MB
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Halibut_finalgenome_mindp15_24chrom_ming90_noabcluster.fam
24.49 KB
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Halibut_finalgenome_mindp15_24chrom_ming90_noabcluster.map
2.32 MB
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Halibut_finalgenome_mindp15_24chrom_ming90_noabcluster.ped
269.79 MB
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Halibut_finalgenome_mindp15_24chrom_ming90.fam
24.89 KB
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Halibut_finalgenome_mindp15_24chrom_ming90.map
2.32 MB
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Halibut_finalgenome_mindp15_24chrom_ming90.ped
274.10 MB
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Halibut_finalgenome.snps.vcf
4.31 GB
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Halibut_genome2_d15gt90HWE_NOCHR1518.fam
23.90 KB
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Halibut_genome2_d15gt90HWE_NOCHR1518.map
2.04 MB
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Halibut_genome2_d15gt90HWE_NOCHR1518.ped
232.17 MB
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Halibut_genome2_d15gt90HWE12_NOCHR1518_LE.fam
23.90 KB
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Halibut_genome2_d15gt90HWE12_NOCHR1518_LE.map
1.59 MB
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Halibut_genome2_d15gt90HWE12_NOCHR1518_LE.ped
181.06 MB
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Halibut_genome2_d15gt90HWE12_NOCHR1518_singleRAD.fam
23.90 KB
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Halibut_genome2_d15gt90HWE12_NOCHR1518_singleRAD.map
770.30 KB
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Halibut_genome2_d15gt90HWE12_NOCHR1518_singleRAD.ped
87.85 MB
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Halibut_metadata_main.txt
47.72 KB
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Metadata_Halibut_ENV_noNAnoWF.txt
355.13 KB
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README
1.34 KB
Abstract
Characterizing the nature of genetic differentiation among individuals and populations and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and commercially important fish species, yet knowledge of population structure and genomic diversity in this species remains lacking. Here, we use restriction-site associated DNA sequencing and a chromosome-level genome assembly to identify over 86,000 single nucleotide polymorphisms mapped to 24 chromosome-sized scaffolds, genotyped in 734 individuals across the Northwest Atlantic. We describe subtle but significant genome-wide regional structuring between the Gulf of St. Lawrence and adjacent Atlantic continental shelf. However, the majority of genetic divergence is associated with a large putative chromosomal rearrangement (5.74 megabases) displaying high differentiation and linkage disequilibrium, but no evidence of geographic variation. Demographic reconstructions suggest periods of expansion coinciding with glacial retreat, and more recent declines in Ne. This work highlights the utility of genomic data to identify multiple sources of genetic structure and genomic diversity in commercially exploited marine species.
bestRAD libraries 768 Atlantic Halibut prepared using the sbfI enzyme, demultiplxed and adapter trimmed, genotyped using stacks2.
Data described in README file