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Orca Genome Reveals New Information on Population Divergence

NEW YORK (GenomeWeb) – A team of researchers led by scientists at Uppsala University in Sweden resequenced and analyzed the genomes of 50 orcas (Orcinus orca) from five different ecotypes to learn more about how genetics influenced their divergence from one another.

Orcas are the largest member of the dolphin family (Delphinidae), and live in all ocean basins across the northern and southern hemisphere from the Antarctic to the Arctic. They're highly social creatures, so genomic population studies have the potential to elucidate the reasons behind their social and environmental adaptations.

Currently, there are more than six known orca ecotypes — they've adapted to different environments and have evolved to consume very different diets that include birds, fish, mammals, and reptiles. Trying to identify where these adaptations are done by selection versus genetic mutation is very difficult to see in genomewide data, first author Andrew Foote, a research fellow at the University of Uppsala, told GenomeWeb.

The study, published in Nature Communications, found that there were several key differences in genes related to protein metabolism and skin regeneration that may shed light on how each ecotype adapts to its unique environment and diet.

The researchers extracted DNA from skin biopsies of free-ranging orcas collected using projected biopsy darts, and created Illumina sequencing libraries built on sheared DNA extracts. The sample set included 10 'resident,' 10 'transient,' seven type B1, 11 type B2, and 10 type C orcas.

The team generated low coverage whole-genome resequencing data for 48 samples using the Illumina HiSeq 2000, and additionally accessed high-coverage sequencing data for two more individual orcas from previous studies. They then mapped the sequence reads to a high-quality, 2.249 Mb reference orca genome assembly from GenBank, and reconstructed the ancestral state for each site by mapping the whole genomic Illumina sequencing reads of the bottlenose dolphin — the orca's closest living relative — to the orca reference genome.

Based on their analysis of the ancestral state reconstruction, the researchers estimated that the time to the most recent common ancestor for these different ecotypes was approximately 126,000 to 227,000 years ago. This estimate overlaps with a recent RAD-seq study published in Heredity in 2015, which estimated the time to the most recent common ancestor at 189,000 years ago.

However, despite the relatively recent common ancestry, the researchers' analysis of the orca genomes indicated that there was substantial genome-wide differentiation and divergence. While all three Antarctic orca ecotypes showed signs of recent relatedness, there was no recent identity-by-descent ancestry detected between the Antarctic and Pacific types or between the sympatric resident and transient ecotypes, the researchers noted.

"[The study looked at] two different locations with ecotype divergence in each location, and it seemed the ecological divergences happened independently," Foote said. The team further noted in its paper that these findings are consistent with strong genetic drift following a demographic expansion from small founding groups.

While determining whether certain genes actually played a role in adaptation is difficult, the researchers noted that there were distinct genomic signatures that indicated climate and diet adaptations. FAM83H — a gene thought to be important for skin development and regulation — may have changed in killer whales with Antarctic lineages to provide slower skin regeneration cycles, which would be necessary for species living in cold water climates. However, Foote added, there are also some behavioral patterns that are unique to this orca ecotype that may have an influence on in its skin regeneration cycle.

The researchers also noted some dietary variation linked with genes such as CES2, which encodes a major intestinal enzyme and has a role in fatty acyl and cholesterol ester metabolism in humans and other mammals. Further, the investigators found indications that predominantly mammal-eating ecotypes — such as the North Pacific transient and Antarctic type B1 — showed signature selection in genes that may play a key role in regulating the methionine cycle, which is critical for metabolizing important proteins that orcas' bodies can't produce on their own.

"It is a complex interaction between the learning history [of orcas] and the adaptation. A lot of previous studies tried to pin it down on one variable," Foote said. In this study, he added, the team was "trying to put together a sort of jigsaw" to see where genomics fit into the equation alongside other ecological and behavioral influences.