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. 2014 May;31(5):1121-31.
doi: 10.1093/molbev/msu058. Epub 2014 Feb 4.

Killer Whale Nuclear Genome and mtDNA Reveal Widespread Population Bottleneck During the Last Glacial Maximum

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Free PMC article

Killer Whale Nuclear Genome and mtDNA Reveal Widespread Population Bottleneck During the Last Glacial Maximum

Andre E Moura et al. Mol Biol Evol. .
Free PMC article

Abstract

Ecosystem function and resilience is determined by the interactions and independent contributions of individual species. Apex predators play a disproportionately determinant role through their influence and dependence on the dynamics of prey species. Their demographic fluctuations are thus likely to reflect changes in their respective ecological communities and habitat. Here, we investigate the historical population dynamics of the killer whale based on draft nuclear genome data for the Northern Hemisphere and mtDNA data worldwide. We infer a relatively stable population size throughout most of the Pleistocene, followed by an order of magnitude decline and bottleneck during the Weichselian glacial period. Global mtDNA data indicate that while most populations declined, at least one population retained diversity in a stable, productive ecosystem off southern Africa. We conclude that environmental changes during the last glacial period promoted the decline of a top ocean predator, that these events contributed to the pattern of diversity among extant populations, and that the relatively high diversity of a population currently in productive, stable habitat off South Africa suggests a role for ocean productivity in the widespread decline.

Keywords: Cetacea; demographics; genomics; population bottleneck.

Figures

F<sc>ig</sc>. 1.
Fig. 1.
PSMC plot for North Pacific killer whale genome (a) and North Atlantic sequence (b) from Genbank (SRA058929; note difference of scale—adjusted to make confidence limits clear) showing confidence limits. Gray bars indicate the interglacial periods following Pleistocene terminations (indicated by Roman numerals). Time ranges for interglacial periods displayed (in years before present): I: 0–14,000; II: ∼115,000–130,000; III: ∼220,000–243,000; IV: ∼320,000–337,000; V: ∼400,000–424,000. g and μ represent the generation time and mutation rate (/nucleotide site/year) assumed, respectively.
F<sc>ig</sc>. 2.
Fig. 2.
Density distributions for heterozygous sites per 50,000-bp bins for draft genome sequences comparing the killer whale and rhesus monkey (a) and comparing the two killer whale genomes (b).
F<sc>ig</sc>. 3.
Fig. 3.
Median joining network based on mtDNA control region fragment. Illustration shows the relationship among haplotypes, but not haplotype frequencies (see supplementary table S1 [Supplementary Material online] which lists haplotype names and accession numbers by number illustrated in the figure), with yellow indicating South African samples, blue Antarctic, and green the rest of the world. The red dots indicate hypothetical haplotypes not found in the data set, while the black dots indicate that there are two steps in those branches. The figure shows the location of global sample sites (see supplementary tables S1 and S2 [Supplementary Material online] for more detail).

Comment in

  • Orca's survival during the ice age.
    Caspermeyer J. Caspermeyer J. Mol Biol Evol. 2014 May;31(5):1325. doi: 10.1093/molbev/msu066. Epub 2014 Mar 5. Mol Biol Evol. 2014. PMID: 24600051 No abstract available.

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