Using poop to identify individual killer whales

DNA can answer many questions about a killer whale’s health and family tree.

Have you ever found yourself riveted to a book or show where all the pieces of a crime are being put together to solve the case? Sometimes, DNA analysis provides a key piece to confidently put the suspect at the scene of the crime. In a similar way, Raincoast scientists carry out very similar work to identify individual killer whales with the array of samples we collect during our photogrammetry field seasons. Now, despite the name, these killer whales aren’t guilty of anything except for enjoying a meal of wild salmon and then expelling the waste, but that fecal waste contains a treasure trove of valuable health information and we need to know exactly which whale it came from.

You may have heard that the DNA between any two people is over 99.9% identical, and that number is in a similar or higher range for killer whales. While that may make it seem tricky to tell individuals apart based on DNA sequence, there are so-called “hotspots” of differences in DNA where we see plenty of variation, and one of these types of differences is called a Single Nucleotide Polymorphism, or SNP for short.

Our Cetacean Research Program spends several weeks each summer taking detailed measurements of killer whale body condition using drones. In partnership with Fisheries and Oceans Canada, poop samples are collected during the same period and analyzed for a number of health indicators like stress hormones and gut health. Those same poop samples are a goldmine when it comes to DNA from the whale that defecated.

Small container filled with brown liquid.
Southern Resident Killer whale fecal sample ready for analysis.

In our Conservation Genetics Lab we are able to separate out the killer whale DNA, make millions of copies of the “hotspot” regions that contain differences between individuals, and then match that information with a database that we and partners have built over several years. This helps to link our drone photogrammetry data and the hormone/health information from Fisheries and Oceans Canada to a specific whale.

How it works

Here is an example of how this works. After using our in-house DNA sequencer, we get the sequence at 68 different SNP locations. Only 26 are shown below to simplify things, but at each location we get the DNA sequence on a chromosome that came from the particular killer whale’s mother, and the chromosome that came from the father: 

We then compare that pattern of DNA SNP sequences to our database that contains almost all Southern Resident killer whales and a majority of Northern Resident killer whales. The SNP sequences for J38 (Cookie), a 20 year old male SRKW, and L82 (Kasatka), a 32 year old female SRKW are shown below.

By aligning these sequences, also known as a genetics fingerprint, we can score each SNP site to see how they match and come up with a positive ID for the killer whale poop sample, with positive matches highlighted in black, and mismatches in orange.

This fecal sample collected during our last field season is a perfect match for L82. Having a match is valuable to help match our poop samples to individual whales, but we can also look at a number of other things as well. As you may know, the maternal pod structure of resident killer whales helps to establish mother/calf relationships, but paternity is another matter. Without DNA we really can’t be sure who the father of a calf is even with observational data like associations or even mating attempts. By comparing genetic fingerprints we can confirm mother/calf relationships and determine paternity as well. 

While this set of studies is important to link the health data from our photogrammetry team and stress hormone data from Fisheries and Oceans Canada to a specific whale, it’s not all that these poop samples can give us. Stay tuned for an upcoming article on determining diet from these same samples.

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Research scientist, Adam Warner conducting genetics research in our genetics lab.
Photo by Alex Harris / Raincoast Conservation Foundation.