Genome sequences can reveal the extent of inbreeding in small populations. Here we present the first genomic characterization of type D killer whales, a distinctive eco/morphotype with a circumpolar, subantarctic distribution. Effective population size is the lowest estimated from any killer whale genome and indicates a severe population bottleneck. Consequently, type D genomes show among the highest level of inbreeding reported for any mammalian species (F_ROH  0.65). Detected recombination events of different haplotypes are up to an order of magnitude rarer than in other killer whale genomes studied to date. Comparison of genomic data from a museum specimen of a type D killer whale that stranded in New Zealand in 1955, with three modern genomes from the Cape Horn area, reveals high covariance and identity-by-state of alleles, suggesting these genomic characteristics and demographic history are shared among different social groups within this morphotype. Limitations to the insights gained in this study stem from the non-independence of the three closely related modern genomes, the short coalescence time of most variation within the genomes, and the nonequilibrium population history which violates the assumptions of many model-based methods. Long-range linkage disequilibrium and extensive runs of homozygosity found in type D genomes provide the potential basis for coupling of genetic barriers to gene flow with other killer whale populations, and the distinctive morphology. 

This alignment is primarily comprised of the 158 unique mitochondrial genome haplotypes from Morin et al. 2015  https://doi.org/10.1111/mec.13284, with the addition of three identical sequences derived from DNA extracted from three type D killer whales as described in the Foote et al. manuscript associated with this submission. The metadata associated with the Morin et al. (2015) dataset are available here: https://datadryad.org/stash/dataset/doi:10.5061/dryad.fm4mk.

Type D mitogenome sequences were generated as follows. Reads were mapped using BWA-MEM to the previously generated mitogenome sequence of the New Zealand type D specimen (accession KF164610; Foote et al. 2013). In a previous study of 139 killer whale mitogenome sequences (Morin et al. 2010), the inclusion of intra- and inter-lab PCR, library build, and sequencing replicates identified inconsistencies in the assembly of polynucleotide repeat regions: one of between nine and 14 Cs in a row (positions 1130–1144 in the original alignment), and another region of seven to eight As in a row (positions 5210–5217). Morin et al. (2010) therefore shortened these to a fixed set of nine Cs and seven As, respectively, to avoid introducing potentially erroneous variation into phylogenetic analysis in that and subsequent follow-up studies (e.g. Foote et al. 2013; Morin et al. 2015). We follow this same conservative approach in our mapping of mitogenomes and identification of sequence variation in this study. 

Foote, A. D., P. A. Morin, R. L. Pitman, M. C. Avila-Arcos, J. W. Durban, A. van Helden, M.-S. Sinding, and T. P. Gilbert. 2013. Mitogenomic insights into a recently described and rarely observed killer whale morphotype. Polar Biology 36:1519–1523.

Morin, P. A., Archer, F. I., Foote, A. D., Vilstrup, J., Allen, E. E., Wade, P., ... & Harkins, T. (2010). Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome research, 20(7), 908-916.