Baleen whale whole-genome VCF data aligned to chromosome-level assemblies of Rice's whale (Balaenoptera ricei) and blue whale (B. musculus)
Data files
Jun 23, 2026 version files 85.37 GB
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Balaenoptera_jointBlueWhale_PASS_SIFT_chr_variants.vcf.gz
1.86 GB
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briceiOutgroupAll_PASS_chr1.vcf.gz
6.18 GB
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briceiOutgroupAll_PASS_chr1.vcf.gz.tbi
180.65 KB
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briceiOutgroupAll_PASS_chr10.vcf.gz
3.61 GB
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briceiOutgroupAll_PASS_chr10.vcf.gz.tbi
101.78 KB
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briceiOutgroupAll_PASS_chr11.vcf.gz
3.74 GB
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briceiOutgroupAll_PASS_chr11.vcf.gz.tbi
100.67 KB
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briceiOutgroupAll_PASS_chr12.vcf.gz
3.21 GB
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briceiOutgroupAll_PASS_chr12.vcf.gz.tbi
88.15 KB
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briceiOutgroupAll_PASS_chr13.vcf.gz
3.13 GB
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briceiOutgroupAll_PASS_chr13.vcf.gz.tbi
88.90 KB
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briceiOutgroupAll_PASS_chr14.vcf.gz
3.24 GB
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briceiOutgroupAll_PASS_chr14.vcf.gz.tbi
87.77 KB
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briceiOutgroupAll_PASS_chr15.vcf.gz
3.11 GB
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briceiOutgroupAll_PASS_chr15.vcf.gz.tbi
84.76 KB
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briceiOutgroupAll_PASS_chr16.vcf.gz
3.11 GB
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briceiOutgroupAll_PASS_chr16.vcf.gz.tbi
97.56 KB
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briceiOutgroupAll_PASS_chr17.vcf.gz
2.73 GB
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briceiOutgroupAll_PASS_chr17.vcf.gz.tbi
78.90 KB
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briceiOutgroupAll_PASS_chr18.vcf.gz
2.80 GB
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briceiOutgroupAll_PASS_chr18.vcf.gz.tbi
77.08 KB
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briceiOutgroupAll_PASS_chr19.vcf.gz
2.18 GB
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briceiOutgroupAll_PASS_chr19.vcf.gz.tbi
59.60 KB
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briceiOutgroupAll_PASS_chr2.vcf.gz
6.04 GB
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briceiOutgroupAll_PASS_chr2.vcf.gz.tbi
172.73 KB
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briceiOutgroupAll_PASS_chr20.vcf.gz
2.29 GB
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briceiOutgroupAll_PASS_chr20.vcf.gz.tbi
57.49 KB
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briceiOutgroupAll_PASS_chr21.vcf.gz
1.36 GB
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briceiOutgroupAll_PASS_chr21.vcf.gz.tbi
36.37 KB
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briceiOutgroupAll_PASS_chr3.vcf.gz
5.80 GB
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briceiOutgroupAll_PASS_chr3.vcf.gz.tbi
168.42 KB
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briceiOutgroupAll_PASS_chr4.vcf.gz
4.87 GB
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briceiOutgroupAll_PASS_chr4.vcf.gz.tbi
144.80 KB
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briceiOutgroupAll_PASS_chr5.vcf.gz
4.67 GB
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briceiOutgroupAll_PASS_chr5.vcf.gz.tbi
135.96 KB
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briceiOutgroupAll_PASS_chr6.vcf.gz
3.90 GB
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briceiOutgroupAll_PASS_chr6.vcf.gz.tbi
114.82 KB
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briceiOutgroupAll_PASS_chr7.vcf.gz
3.92 GB
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briceiOutgroupAll_PASS_chr7.vcf.gz.tbi
110.66 KB
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briceiOutgroupAll_PASS_chr8.vcf.gz
3.73 GB
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briceiOutgroupAll_PASS_chr8.vcf.gz.tbi
107.25 KB
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briceiOutgroupAll_PASS_chr9.vcf.gz
3.74 GB
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briceiOutgroupAll_PASS_chr9.vcf.gz.tbi
106.38 KB
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briceiOutgroupAll_PASS_variants_chr.vcf.gz
6.15 GB
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README.md
2.47 KB
Abstract
This dataset contains whole-genome sequencing data processed as variant call format (VCF) files for 37 baleen whale individuals representing six species: Rice's whale (Balaenoptera ricei, n = 25), Bryde's whale (B. edeni edeni, n = 2; B. edeni brydei, n = 4), sei whale (B. borealis, n = 1), blue whale (B. musculus, n = 1), and fin whale (B. physalus, n = 4). All individuals were mapped to two chromosome-level reference assemblies — the Rice's whale (B. ricei) and blue whale (B. musculus) — yielding two parallel VCF datasets for comparative genomic analyses. These data support phylogenomic and population genomic investigations of the Bryde's whale species complex, including assessment of species boundaries, mito-nuclear discordance, and the evolutionary distinctiveness of the critically endangered Rice's whale.
Dataset DOI: 10.5061/dryad.s7h44j1q5
Description of the data and file structure
Whole-genome sequencing data were generated for 24 Rice's whales (Balaenoptera ricei), a critically endangered species restricted to the Gulf of Mexico, using tissue samples obtained via biopsy and stranding events collected between 1992 and 2024. To provide comparative context for population genetic and demographic analyses, additional whole-genome sequencing data were compiled for closely related rorqual species, including Eden's whale (B. e. edeni), Bryde's whale (B. e. brydei), sei whale (B. borealis), blue whale (B. musculus), and fin whale (B. physalus), drawing on both newly sequenced samples and previously published genomes (DNAZoo, Vertebrates Genome Project, and other studies). These data support analyses of genetic diversity, population structure, and demographic history within Rice's whales and across the broader Balaenoptera genus, with implications for the species' conservation status.
Files and variables
File: briceiOutgroupAll_PASS_variants_chr.vcf.gz
Description: Genome-wide variant call file (all chromosomes combined) for the full sample set — Rice's whale (Balaenoptera ricei) individuals plus outgroup taxa (Eden's whale, Bryde's whale, sei whale, blue whale, and fin whale) — with reads mapped to the Rice's whale reference genome. Includes PASS-filtered variants only.
File: Balaenoptera_jointBlueWhale_PASS_SIFT_chr_variants.vcf.gz
Description: Genome-wide variant call file (all chromosomes combined) for the same sample set as above — Rice's whale individuals plus outgroup taxa — but with reads mapped to the blue whale reference genome. Includes PASS-filtered variants only, with SIFT annotations predicting the functional consequences of coding-region substitutions.
File: briceiOutgroupAll_PASS_chr[N].vcf.gz (chr1–chr21)
Description: Chromosome [N]. Per-chromosome subset of briceiOutgroupAll_PASS_variants_chr.vcf.gz (Rice's whale reference, full sample set, PASS-filtered variant and invariant sites).
File: briceiOutgroupAll_PASS_chr[N].vcf.gz.tbi (chr1–chr21)
Description: Chromosome [N]. Tabix index for the corresponding VCF file, enabling indexed retrieval of specific genomic regions.