Mitogenome alignment of 159 unique haplotypes representing 455 individual killer whales ...

• Main Author: Foote, Andrew
• Format: Dataset
• Language: English
• Published: Dryad 2022
• Subjects: FOS Biological sciences; killer whale; Orcinus orca; type D; Mitogenome; alignment; Cape Horn; Foote; New Zealand; Killer Whale; Orca; Killer whale
• Online Access: https://dx.doi.org/10.5061/dryad.wpzgmsbr7; https://datadryad.org/stash/dataset/doi:10.5061/dryad.wpzgmsbr7

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 ... : 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 ...