Supporting Data for: Ocean-wide conservation genomics of blue whales suggest new Northern Hemisphere subspecies

The blue whale is an endangered and globally distributed species of baleen whale with multiple described subspecies assignments, including the morphologically and molecularly distinct pygmy blue whale, among others. North Atlantic and North Pacific populations, however, are currently regarded as a single subspecies despite being separated by continental land masses and differences in their acoustic communication. To determine the degree of isolation among the Northern Hemisphere populations, fourteen North Pacific and six Western Australian blue whale nuclear and mitochondrial genomes were sequenced and analyzed combinedly with eleven publicly available North Atlantic blue whale genomes. This allowed to contrast the genetic differentiation and genetic exchange among Northern Hemisphere populations to the Western Australian pygmy blue whale subspecies. Population genomic analyses revealed distinctly differentiated clusters and limited exchange among all three populations, indicating a hi..., We sequenced the genomes from 20 blue whale specimens gathered from the North Pacific blue whale and West-Australian pygmy blue whale populations and analyze the data together with 12 publicly available genomes of other blue whales, including those of the North-Atlantic blue whales (Jossey et al., 2024). This sampling is further complemented by three genomes of the closely related sei whale (Balaenoptera borealis), of which one is sequenced in this study.
All Illumina paired-end libraries were prepared by Novogene, Cambridge, United Kingdom using the NEBNEXT DNA LIBRARY PREP kit with a read length of 150 base pairs (bp) and an insert size of 350 bp. Illumina sequencing was performed on a NovaSeq 6000 platform targeting ~20x coverage per individual.
A comprehensive pipeline used to process the data and perform many of the here presented downstream analyses can be found on GitHub: mag-wolf/RESEQ-to-Popanalyses/.
Short read data were trimmed for quality and adapter sequences using FASTP V0..., Usage Notes:
All variance sets are contained in zipped vcf files and might be viewed and altered with BCFTOOLS (Danecek et al., 2021). While the genome wide set only contains SNPs, the haploid mitochondrial and sex-chromosomal data contain also conserved sites!, # Supporting Data for: Ocean-wide conservation genomics of blue whales suggest new Northern Hemisphere subspecies

\[Access this dataset on Dryad: [https://doi.org/10.5061/dryad.47d7wm3jz](https://doi.org/10.5061/dryad.47d7wm3jz)]

We sequenced the genomes from 20 blue whale specimens gathered from the North Pacific blue whale and West-Australian pygmy blue whale populations and analyze the data together with 12 publicly available genomes of other blue whales, including those of the North-Atlantic blue whales (Jossey et al., 2024). The data was used for SNP calling of genomic, mitogenomic, mt_Marker region, and y-chromosomal data. The SNPs were subsequently used for population genetic analyses regarding gene flow, genetic divergence, phylogenetic reconstruction and genetic viability.

## Description of the data and file structure

In this data repository, we provide filtered, high-quality SNPs called from our genomic resequencing and subsequent mapping to the blue whale reference genome...