Showcase Tag: Animal Behavior

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.”

The Physics of Fox Movement in Complex Landscapes

Sheldon Opps recalls watching a large silver fox from the window of his Prince Edward Island home last winter. The fox in question was navigating the urban sidewalk, maneuvering around high snowbanks, even pausing to check for traffic before crossing the street. “He was tracing a path just like a human would,” Opps says. “He was very comfortable in his urban environment.” Opps spends a lot of time thinking about urban foxes. The University of Prince Edward Island physics professor has been conducting an ongoing study of fox movement patterns within highly fragmented habitats such as urban Charlottetown. But Opps is not a biologist. He’s an expert in the field of soft condensed matter physics, where he applies the tools of statistical physics to study a variety of biologically relevant physical systems, including liquids, colloids, foams, gels and biological tissues. The interest in fox behaviour came via his wife Marina Silva-Opps, a biologist at UPEI, and from his interest in applying the methods of computational and statistical physics to study other complex systems – such as animal movement. The life of a fox in Charlottetown is fraught with challenges. Along with the typical dangers that a city presents – traffic, hostile dogs and homeowners, a lack of natural food sources – the animals must deal with ever increasing habitat fragmentation that breaks up their traditional hunting grounds. Opps is studying what that fragmentation means for both foxes and humans. Habitat fragmentation is having some unusual effects on the highly adaptive fox population. For one thing, the animals are quickly becoming semi-domesticated as homeowners feed them and even give them names in many cases. “We’re seeing the same patterns happening that we believe led to the domestication of dogs thousands of years ago,” says Opps. According to the current theory, wild wolves began living in close proximity to humans in the Palaeolithic age to take advantage of their hunting leftovers, eventually becoming domesticated by the process. “The conjecture is that in 50 or 100 years, if this continues, foxes could become domesticated here in Charlottetown as they have in other areas in the world, such as Russia”. Patrick Strongman is a physics undergraduate student at UPEI and an ACENET fellowship holder who is working with Opps on the fox project. As part of his research project, Strongman developed the algorithm used to track fox movements and identify cluster points where animals gathered. The algorithm compiled hundreds of data points including individual fox movements, distances travelled, velocity and GPS information, and used the data to run simulations of fox movements based on changing urban conditions. Strongman says the ACENET computer network was key to the project. “It cut down to a few hours what would have normally taken weeks to complete,” he says. Opps admits that fox habitat is an unusual subject for a physicist to be studying – particularly one trained in theoretical disciplines such as quantum mechanics and statistical physics. But he says it’s not really such a big stretch. “Like any physicist I’m a problem solver,” he says. “Physicists are usually busy looking across time and space or peering down into the realm of quantum mechanics. But just as a telescope looks back into time to study the beginnings of the universe, a study like this can unlock the secrets of how life evolved over time. Everything is interconnected. Humans and foxes are all a part of an evolving universe.”