When a dead killer whale washes up on a beach in British Columbia, the first thing we try to determine — along with why it died in the first place — is who it is. Almost all killer whales that spend time in B.C. waters have been identified and in most cases we know a fair bit about them: the population they belong to, how old they are, and who their mothers and offspring are. Carcasses are often too decomposed to match to the photo collection, in which case we turn to genetics, just like forensic investigators working on human cases.
Dr. Lance Barrett-Lennard, senior marine mammal scientist at the Vancouver Aquarium Marine Science Centre’s Coastal Ocean Research Institute, is B.C.’s leading expert on killer whale genetics. So when such a carcass washes up, he usually gets a call. In turn, he asks me and Allyson Miscampbell — both molecular biologists in the Institutes’ Conservation Genetics Lab — to do the necessary lab work to make the genetic match. This is exactly what we were called on to do last week when two killer whales carcasses were found at two different locations in B.C. The first was a newborn female calf, too young to have been photo-identified, and the second, an adult male, was in a sufficient state of decomposition that identification based on appearance was impossible. Both killer whales had been necropsied (similar to a human autopsy) by staff from the BC Animal Health Centre, and from Fisheries and Oceans Canada.
Following the first necropsy on the calf, a colleague from Fisheries and Oceans Canada dropped off a small piece of skin for us to analyze at the Aquarium. A few days later, I had already started extracting DNA from the sample when I learned of another killer whale death, this time the adult male. A necropsy was scheduled for Friday and I made arrangements with the pathologist to get a piece of skin from the adult male. Understanding the urgency in this case, I picked up the skin sample on Sunday and rushed back to the lab to get to work. Now it was time to play catch up — the most timely and cost-effective way to analyze both samples is to run them together, so I had to work fast and at odd hours to bring both the young female and the adult male to the same stage in the process.
The process of going from a piece of skin to DNA results takes several days. The first step is to extract DNA from the cells in the skin samples, a process with a number of steps that takes about 30 hours to produce a drop of pure DNA. It’s akin to baking: you need to follow a very strict set of instructions and won’t know for certain how it’s going to turn out until you’re finished. Our colleagues at Fisheries and Oceans were keen for answers as soon as possible; because time was of the essence, we wanted to avoid problems that would force us to repeat steps or start over. In the same way you would tweak a recipe in baking cookies — try a small batch with butter instead of oil, try a batch with two eggs instead of one etc. — this is what we did for our samples. I divided the DNA from each whale into subsamples, repeated the “recipe” with minor variations, and then selected the results that worked best. Tweaking the recipes and looking at each option kept me busy into the wee hours of the morning, but it put us in a good position to determine population identities by the following night.
Allyson Miscampbell then picked up the samples and took them to the Genetic Data Centre at UBC to sequence enough of the genetic code to determine which population each whale belonged to. She went through a number of steps and “loaded” the samples into a high-tech DNA sequencing machine. She began to watch the sequence unfold, knowing it would be many hours before it was complete.
Lance has discovered 13 variations in the genetic code that can be used to reliably distinguish killer whale populations, and Allyson had to wait for 10 hours for all of them to reveal themselves. By late afternoon, the sequence was sufficiently complete to tell that both whales were of the fish-eating “resident” variety, but it was nearly 11 p.m. before the last part of the sequence showed that both belonged to the southern resident population. It was great to have a definitive result but the feeling was bittersweet — the southern resident population is endangered, and with less than 85 members, it is at far greater risk than the other killer whale populations found in B.C.
Despite long days and some long nights last week, identifying these two whales gave us a great opportunity put the new Conservation Genetics Lab through its paces. Working quickly, knowing that many scientists, conservationists and members of the public would be interested in our findings upped the excitement level. We hope it will be some time before any more killer whales wash up on our shores. But when they do, we’re ready.
Blog post by Carla Crossman, molecular and marine biologist with the Vancouver Aquarium Marine Science Centre’s Coastal Ocean Research Institute.
Coastal Ocean Research Institute
Established to measure and monitor the health of coastal ecosystems on Canada’s West Coast, the Coastal Ocean Research Institute, part of Vancouver Aquarium Marine Science Centre, is a multi-disciplinary, collaboration-based Institute established to increase dialogue and inform policy. The Research Institute is grateful for its generous founding funding partners Sitka Foundation and North Growth Foundation.