Humpback whale genomes reflect the increased efficiency of commercial whaling

Genetic diversity is declining globally, a trend that may particularly impact exploited populations that must adapt to rapid environmental change and other threats. Estimated genomic changes in effective population size mirrored known whaling history and shifts in technology. In the Southern Ocean, a comparison of genomes from historical and contemporary populations indicated that the contemporary genomes have less diversity and an elevated realised mutation load for moderately deleterious mutations, likely due to the effects of whaling. Our results demonstrate that the relatively recent, brief, and drastic depletion of humpback whale populations by whaling likely had subtle but discernible, negative, and lasting effects on the whales’ genomes. Thus, even as some humpback whale populations are now recovering to pre-exploitation numbers, they likely do so with a diminished adaptive capacity in the face of future conditions and threats.
, , # Humpback whale genomes reflect the increased efficiency of commercial whaling

Dataset DOI: [10.5061/dryad.37pvmcvwx](10.5061/dryad.37pvmcvwx)

## Description of the data and file structure

Data collected for the humpback whale genomic assessment in the North Atlantic and Southern Ocean. 

### SNP VARIANT FILES

#### File: SOU_contemporary_data.snps.vcf.gz

**Description:** Variant file for the contemporary Southern Ocean genomes only. 

#### File: NAT.contemporary.filter.vcf.gz

**Description:** Variant file for the contemporary North Atlantic genomes only. 

#### File: downsampled.temporal.all.vcf.gz - (downsampled.temporal.all.vcf.gz.tbi)

**Description:** Variant file for temporal comparisons using the downsampled dataset, including all samples (used for genetic clustering estimates)

#### File: downsampled.temporal.final.filtered.vcf.gz

**Description:** Variant file for temporal comparisons using the downsampled dataset, excluding samples with lower average depth (used for gene...,