Small pieces of marine species in seal faeces

I try to stay out of the fur seal diet. Image from Julie Paterson.

It’s always intriguing discovering what people like to eat. Eating is a reasonably private process. Sure we can go out for meals with friends or grab a bite with colleagues but we are choosing from a restricted menu (and the food on offer is different to what you would have access to normally anyway). Most food is consumed at home or in some private nook. If I was asked to name what usual food my friends consumed I would be in some trouble. Of course diet changes over time, during the course of a life, with the changing seasons, even during the week. As a child growing up on a farm we had plenty of mutton roasts, casseroles, lambs fry and bacon and potatoes. As an adult I have a lot more rice, sushi and chicken.

Sharing a meal with people, especially a pot luck meal (where everyone brings whatever they want) is a nice way of finding out more about the private lives of these friends. What spices do they use? Do they spend time on presentation? How healthy are the ingredients?

Arsalan searching for fresh fur seal ‘diversity survey capsules’. Image from Adrian Paterson.

Finding out what animals eat is also a challenge. Sometimes, it’s relatively easy. You can follow grazing herbivores at a distance and see what they are chomping on. Most species are a lot more discrete about eating or eat at inconvenient times (e.g. in the dark) or places (e.g. the canopy of trees). It can be a challenge to the researcher to figure out the diet of their species. Which is a shame as it can be vitally important information.

Marine animal diets can be especially difficult to figure out. Most of their eating occurs in dim water far from an observer. The New Zealand fur seal is an example of this. NZ fur seals are a species rushing back from the edge of extinction. Their numbers are growing so quickly that they are coming into conflict with fishers who feel that the increasing populations are competing with them for preferred fish species.

How can we answer this question about what they eat. We could look at stomach contents (either from dead seals or from encouraging them to vomit up the contents) or we could look in their faeces to see what we can find. Unfortunately, these methods miss a large number of the species eaten as one small piece of tissue looks like another.

Enter DNA. Although DNA is broken down during the digestion process, small sections of DNA chains can survive through to being deposited back into the environment in faeces. The good thing about DNA is that it can often identify the species that it came from, even when so degraded. A seal poo is really a potentially excellent sampling device (a diversity survey capsule if you will) for what an individual ate while swimming around the ocean.

Arsalan Emami-Khoyi and colleagues, including Adrian Paterson, Rob Cruickshank and James Ross, collected seal faeces from colonies around New Zealand and used a technique called massively parallel sequencing to identify what species had been eaten. This approach allows all of the DNA in the sample, and from all of the species present, to be obtained in one shot and is ideally suited for this kind of question. The research has been published in Conservation Genetics Resources.

Fur seal faeces… There is DNA from over a dozen marine species in there! Image from Adrian Paterson.

The major finding was that seals seem to eat pretty much anything that they come across. Samples pooled from each colony showed that up to 46 fish species and 18 squid and octopi species were taken at any one site. Colonies differed hugely between areas and even at different times of the year in the same colony. Sharks and other cartilaginous fish seemed to be more important than previously thought to fur seals and there is evidence that they can predate even very large sharks where they take just the choice parts (livers and stomachs).

Fur seals did take commercial fish species although they only made up about 10% of the species consumed. However, this DNA method does not tell us how common a species was in the poo. The commercial species might make up 80% of the numbers consumed or 8%. So there is potential for conflict with human fishers. On the upside, given that the seals appear to be very generalist feeders, it seems unlikely that they would focus on any particular species.

This new DNA approach to identifying diet through analyzing faeces looks very promising for shedding light on cryptic species. However, I think I still prefer the pot-luck dinner approach for figuring out what my friends like.

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