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Mitochondrial DNA Points to Multiple Killer Whale Species

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Killer whale "ecotypes," which vary in their choice of prey, behavior, and appearance, represent distinct species, according to a paper appearing online yesterday in Genome Research.

An international research team including researchers from Roche's 454 Life Sciences and Roche Applied Sciences, used highly parallel pyrosequencing to assess the complete mitochondrial genomes of nearly 150 killer whales from the North Atlantic, North Pacific, and southern oceans. In so doing, they identified dozens of mitochondrial haplotypes that point to the existence of at least three killer whale species.

"We recommend that three named ecotypes be elevated to full species, and that two additional types be recognized as subspecies pending additional data," lead author Phillip Morin, a geneticist affiliated with the National Marine Fisheries Service's Southwest Fisheries Science Center and the University of California at San Diego's Scripps Institution of Oceanography, and colleagues wrote.

Killer whales are currently classified as just one species, Orcinus orca. Nevertheless, researchers have identified several so-called killer whale ecotypes that have slightly different size and color patterns, behaviors, prey preferences, and social organizations.

Past studies of specific mitochondrial DNA loci have found relatively little mtDNA diversity, the researchers explained, and just over a dozen haplotypes. Nuclear microsatellite data, meanwhile, hints at the existence of additional genetic diversity and more complex population structure than previously appreciated.

"This low level of mtDNA diversity has resulted in only weak inference of phylogeographic patterns and divergence times in killer whales, limiting our ability to understand their evolution and taxonomy," they wrote. "Killer whales are therefore an ideal candidate species for applying new high-throughput techniques to allow the production of a highly corroborated mitogenome tree and the testing of hypotheses of the timing of coalescence of killer whale populations."

To test the taxonomic and evolutionary utility of high-throughput mitogenomics, the team sequenced the 16,390 or so base pairs of mitochondrial genomes from 143 killer whales using highly-parallel pyrosequencing with Roche 454 GS FLX and Titanium platforms. They also sequenced five partial mitochondrial genomes and mtDNA for three outgroup species: a false killer whale, a long-finned pilot whale, and a short-finned pilot whale.

After tossing out duplicate and poor quality sequences, the researchers were left with 139 killer whale mitochondrial genome sequences representing 66 different haplotypes.

These haplotypes clustered with geography and killer whale type, although whales from a few distant geographic populations grouped near one another, the team explained, suggesting they might share common ancestors.

They estimate that killer whale haplotypes identified in the study diverged from one another between around 150,000 and 700,000 years ago, with clades from the eastern North Pacific apparently diverging earliest and an Atlantic clade diversifying into killer whale groups found in high latitudes today.

Based on their mitogenomic findings, the researchers called for a revised killer whale classification scheme designating two existing killer whale types in the Southern Ocean and one group in the North Pacific as distinct species and recognizing additional subspecies. Even so, the researchers noted, studies of nuclear sequence data are needed to verify and further refine the patterns detected so far.

Overall, the team argued, using genetic information to improve killer whale classifications and taxonomy will help to inform killer whale ecology research and conservation efforts in the future. They also predicted that mitochondrial genome sequencing will play an increasingly large role in classifying other species as well.

"We expect that, as sequencing technologies continue to allow more samples, more sequence, and lower cost the application of mitogenomics will become the default approach to phylogeography, as was previously the use of control region and cytochrome B sequence analysis," the researchers concluded.

Sequence data on the 66 killer whale haplotypes identified in the current study have reportedly been deposited in Genbank.

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