Mitogenome alignment of 159 unique haplotypes representing 455 individual killer whales

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 (FROH  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.