DOI: 10.5061/dryad.wpzgmsbr7
title: Mitogenome alignment of 159 unique haplotypes representing 455 individual killer whales

description: 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. 
description: 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.
description: # Title of Dataset: Mitogenome alignment of 159 unique haplotypes
 representing 455 individual killer whales This alignment is primarily
 comprised of the 158 unique mitochondrial genome haplotypes from Morin et
 al. 2015 , 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:
 . 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 11301144
 in the original alignment), and another region of seven to eight As in a
 row (positions 52105217). 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 36:15191523. 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.
 Sharing/access Information Links to other publicly accessible locations of
 the data: Was data derived from another source? If yes, list source(s):
 Morin et al. 2015