DOI: 10.5061/dryad.37pvmcvwx
title: Humpback whale genomes reflect the increased efficiency of commercial whaling

description: 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.
description: # 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
 genetic load, heterozygosity, and ROH estimates). ### GONE RESULTS
 Demographic estimates results from GONE. Files contains three columns:
 first column indicates the replicated run, second column indicates the
 number of generations back in time, and the third column indicates
 effective pop size (NE) estimates.  #### File: NAT.01h.estimates.gone
 **Description:** GONE estimates results for the North Atlantic using
 hc=0.01 #### File: NAT.10h.estimates.gone **Description:** GONE estimates
 results for the North Atlantic using hc=0.10 #### File:
 NAT.05h.estimates.gone **Description:** GONE estimates results for the
 North Atlantic using hc=0.05 #### File: SOU.10h.estimates.gone
 **Description:** GONE estimates results for the Southern Ocean using
 hc=0.10 #### File: SOU.01h.estimates.gone **Description:** GONE estimates
 results for the Southern Ocean using hc=0.01 #### File:
 SOU.05h.estimates.gone **Description:** GONE estimates results for the
 Southern Ocean using hc=0.05 ### PLINK FILES PLINK PED and MAP variant
 files for the different datasets used in the study #### File:
 **:** NAT_contemporary_snps.map **Description:** North Atlantic genomic
 coordinates for contemporary dataset (used as input for GONE) #### File:
 NAT_contemporary_snps.ped **Description:** North Atlantic genomic variants
 for contemporary dataset (used as input for GONE) #### File:
 SOU_contemporary_snps.map **Description:** Southern Ocean genomic
 coordinates for contemporary dataset (used as input for GONE) #### File:
 SOU_contemporary_snps.ped **Description:** Southern Ocean genomic variants
 for contemporary dataset (used as input for GONE) ## Scripts and Codes
 Scripts used in the study are deposited in the associated Zenodo
 repository  #### File: alignment.sh **Description:** script including all
 steps to obtain alignment files from raw reads   #### File: calling.sh
 **Description:** script including all steps to obtain SNPs variants from
 alignment files (unfiltered VCF files) #### File: filtering_genotypes.py
 **Description:** script including all steps to obtain filtered SNPs
 variants (filtered VCF files) #### File: clustering.sh
 **Description:** script including steps to obtain clustering results. It
 includes conversion steps to PLINK files and clustering analyses. ####
 File: gone_runs.sh **Description:** script including steps to obtain
 demographic estimates using GONE from PLINK files.  #### File:
 mutation_load_count.py **Description:** script including steps to
 calculate mutation load counts from VCF files. #### File:
 allele_count_sites.py **Description:** script including steps to calculate
 derived and total alleles from VCF files.  #### File: rxy_calculation.py
 **Description:** script including steps to calculate Rxy statistics from
 allelic counts. ## Access information Other publicly accessible locations
 of the data: Raw data is available under the NCBI project
 code: PRJNA1250286
 ([https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1250286](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1250286)). Outgroup raw data is available under the NCBI BioSample code: SAMN43059233 ([https://www.ncbi.nlm.nih.gov/biosample/SAMN43059233](https://www.ncbi.nlm.nih.gov/biosample/SAMN43059233))