| Summary: | 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. Funding provided by: European Research Council Crossref Funder Registry ID: https://ror.org/0472cxd90 Award Number: ERC-COG-101045346 Funding provided by: NOAA National Marine Fisheries Service Office of Science and Technology Crossref Funder Registry ID: https://ror.org/04950b532 Award Number: Funding provided by: European Union Crossref Funder Registry ID: https://ror.org/019w4f821 Award Number: 663830 This alignment is primarily comprised of the 158 unique mitochondrial genome haplotypes from Morin et al. 2015 ...
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