Seal diet analysis meets big data

“How much salmon do harbor seals eat?” sounds like a simple question, but is actually one of the trickiest to answer. Biologists once answered this question by shooting seals and weighing the different species of fish found in their stomachs. More recently, however, biologists have been minimizing their impact on the seals by identifying and measuring the hard parts of prey found in feces (scats) collected from seal haulouts. Analyzing scats has been suitable for identifying the type and size of prey consumed, but has not yet been effective for determining how much of each prey type a seal has eaten.

A promising alternative technique that might circumvent the problems associated with not being able to estimate quantities consumed from prey bone remains is DNA analysis. It turns out that some DNA from prey fish passes through a seal's gut unharmed and can be detected in the resultant seal scats. It may thus be possible to measure the amounts of different prey species DNA in seal scats to infer the relative amounts of different fish the seals ate.

Harbor sealAs part of his Ph.D at UBC, Austen Thomas is developing a method to determine proportions of prey consumed from quantities of DNA contained in scats. Working with Australian collaborators, he is analyzing small gene fragments of the prey fishes to identify species consumed. He then uses the relative abundance of DNA in the seal scats to calculate the percentage of different speicies of prey in the diet.

Each scat sample provides about 50,000 DNA sequences—and each sequence has to be assigned to a prey species. Thank goodness for computers!

This new DNA technique for quantifying diets relies on the untested assumption that DNA sequence percentages from seal scats are representative of seal diets. To validate this assumption, Austen and his colleagues have conducted a series of feeding and scat collecting experiments with captive harbor seals at the Point Defiance Zoo and Vancouver Aquarium.

Austen’s next step is to take what has been learned from the captive seal feeding trials and apply it to scats collected from wild harbor seals in the Strait of Georgia. With support from the Pacific Salmon Foundation, Austen and a group of dedicated volunteers have collected ~2,000 harbor seal scats from haulouts throughout the Strait over the past three years. These samples are currently being processed at UBC for eventual analysis on a high-throughput DNA sequencer. Austen will then sort through gigabytes of sequence data produced from the scat samples to summarize diets of harbor seals in the Strait of Georgia. By next summer, Austin anticipates having new insights into the age old question of how much salmon harbor seals really eat!

Austen Thomas is a Ph.D candidate at U.B.C.




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