From Megabytes to Megafauna: Driving Whale Conservation to New Depths with High Performance Computing

“I think whales are kind of like dinosaurs,” says Tim Frasier. “Almost everyone is interested in them at some point in their childhood, but some of us don't grow out of it.”

Frasier, now a biology professor at Saint Mary's University in Halifax, Nova Scotia, is following his dream. His lab studies genetic variations in whale populations to fuel conservation efforts using high performance computing (HPC). Their present focus is on the North Atlantic right whale and Saint-Lawrence beluga.

By observing the variability of an individual's genome over its lifetime, Frasier and his students determine how inbreeding and traumatic events, such as ship strikes or entanglement in fishing gear, make individuals and populations less able to recover and reproduce.

The Frasier Lab sequences whale genomes from minuscule pieces of skin collected humanely by field teams. They then compare the variation in gene expression in healthy and injured whales, the life histories of which they know thanks to data collected by researchers through photo-identification over the last several decades. All these data provide the basis to understand how the cumulative effects of inbreeding and multiple stress factors can cause individuals to not reproduce or live as long.

Frasier specifies, however, that these analyses involve millions of DNA fragments, which take up huge amounts of both storage space and computing power. “You just can't do it on a normal computer.” Access to ACENET and the Alliance’s supercomputing facilities are instrumental in enabling his lab to tackle complex genetic analyses that would otherwise be impossible.

Frasier gets asked a lot how this kind of information translates into helping conservation. One way is by influencing policy. Existing legislation imposes limits on different industries according to their impact on whales. For example, a North American right whale hit by a ship or entangled in a fishery somewhere along the east coast of the US and Canada could trigger either a ship slowdown in the area or completely shut down that fishery for the season. He explains that these triggers might only be quantified based on whether the whale died or not, “like a yes-no question.” But if Frasier’s research can show that these incidents change their reproductive success for years afterward, then it would also demonstrate that current measures are vastly insufficient to help populations recover and thrive in the long term.

Frasier's work both advances our understanding of whales and provides a framework for devising more appropriate measures to encourage population recovery. It also highlights the importance of computing resources in modern biology research and conservation. "Without ACENET, we wouldn't be able to do this work," he says. "It's just such a great resource that we have, and many of the geneticists in Canada that I know feel that way."