As a statistician at UNB in Saint John, Connie Stewart works with “pretty much anyone who needs help.” Like a superhero, she swoops in whenever fellow academics have a statistics puzzle to solve. In helping her colleagues, she’s also developing new statistical methods, and these days, most of the time that ground-breaking work happens in concert with ecology-based research. She first started working with ecologists while working on her PhD. She was working with Dalhousie University ecologists and statisticians who developed “quantitative fatty-acid signature analysis” (QFASA) in relation to grey seals. QFASA is a way to estimate seal diets — some fatty acids of the prey the seals ingest end up in the latter’s tissue with little change. QFASA involves statistical methods to match the predator with its prey’s fatty acids. The result — an estimate of the seal’s diet —includes the proportion of each prey species in the seal’s diet. “You get an estimate of diet that might, for example, contain 30 per cent herring, 20 per cent capelin, and so on,” Stewart says. “That’s an estimate. The biologists I’m working with are studying the grey seal population off the coast of Sable Island, but this can be used on a number of species, including polar bears, seabirds and sea lions.” But before she could come up with results for her colleagues, she had to solve a problem. Analyzing the diet estimates wasn’t straightforward because they are constrained to percentages that add up to 100, which means she could not apply standard statistical methods to them. She had to find a way to answer standard ecological questions in a non-standard way. When researchers such as Stewart develop new statistical methods, they run simulations to assess their efficacy. “We generate pseudo-predators, which we can do if we have a prey database,” she says. “You choose a diet of your choice and then you sample from the prey base proportionately. That gives you a pseudo fatty-acid signature.” She then takes that pretend seal fatty-acid signature and can estimate the diet and apply her methods to it. “Because we generated it with a specific diet, we know how good our answers are,” Stewart explains. “In practice, you have data and you can apply any method you want to it, but you don’t know what the true answer is. Here, we know the diets of the pseudo-predators and can see whether our methods are behaving correctly.” Running such simulations takes a long time, so Stewart uses high-powered computing through ACENET and Compute Canada to do her work. She used to use a cluster at Dalhousie University, but she migrated to ACENET’s digital infrastructure because it’s bigger and can accommodate more users working at the same time. Could she do her work without ACENET? “I’d be more limited in the different cases I could run and how long it would take me to get the research done.” As for the grey seals, knowing their diet is important because their population in the Northwest Atlantic has increased from about 15,000 in 1960 to 424,300 in 2016. Ecologists want to understand the impacts of that ballooning population on the overall ecosystem, particularly as it relates to fish populations that are commercially important to the local economy. Stewart’s statistical analyses are helping them get there.
Showcase Tag: Ecology
The Secrets of Birds
Anyone who has watched a flock of birds fly by knows that keeping track of individual birds can be complicated. But what if you had to chart the movements of a whole population of birds using data taken over many years and using different measuring tools and data sources? That’s precisely the challenge that one Acadia biology professor and his graduate student had to tackle. Dr. Mark Mallory and Master’s student Christine Anderson have been studying the migratory movements of herring gulls based on electronic data, and they are using the ACENET computer network to help them with their work. Anderson is using tracking data from a herring gull population in Nunavut and comparing them to other data from places such as the Great Lakes, Brier Island, Sable Island and Newfoundland to find out how each population is behaving differently from the others. It’s a complicated process because the data comes in many forms. Some of it comes from a process called Doppler triangulation that pinpoints the birds’ movements in a range of 350 metres to one kilometre. Other data takes the form of GPS tracking – an accuracy of just a few metres. “With the ACENET system I can input data with different errors and the system will take each error into account and give me an accurate reading,” says Anderson. “It can take up to two weeks to run a program. It’s something I couldn’t possibly do on my laptop.” Mallory says that Anderson is the first of his students to make use of the ACENET system. He says her study has some important practical components that go beyond pure scientific understanding. “First of all, by understanding their movements over time it allows us to identify places where we need to create protected areas for migrating birds. Also, it allows us to understand what these birds do to their environment and how they interact with humans. Are they spending more time over a landfill or over water? Are they creating a danger around airports? Are they picking up diseases like avian influenza that can infect humans? These are important questions.” Anderson says that she doesn’t have a lot of background in computers, but the support she received from ACENET was invaluable. “The ACENET staff are incredibly helpful,” she says. “I couldn’t have done this project without them.”
Deciphering the Role of the Invisible Marine Life
In terms of impact and sheer numbers, microbes dominate our planet. The tiny single-celled organisms invisible to the naked eye live everywhere on Earth – in the atmosphere, the earth’s crust and in our own bodies. The world’s oceans are also teeming with microbes – accounting for more than 90% of the ocean biomass. For Julie LaRoche, microbes represent an important indicator of the effects of climate change on ocean life. LaRoche is a biology professor and ocean scientist at Dalhousie University and the Canada Research Chair in Marine Microbial Genomics and Biogeochemistry. “We study how phytoplankton and marine bacteria are affected by increases in temperature and decreases in pH, changes that are both linked to the increase of carbon dioxide in the atmosphere. Marine microbes are key players in marine biogeochemical cycles or, simply put, they are key players in the recycling of nutrients and other elements in the ocean. Changes in the balance of the recycling will affect the productivity of the ocean, including the higher trophic life – fish and other sea creatures.” Instead of microscopes, LaRoche uses genomics and next generation sequencing techniques to study the diversity and function of ocean microbes. She says the technology has represented a huge leap forward for the science of microbiology. It has led to many discoveries of new taxonomic groups and biochemical pathways in marine microbes since its development a decade ago. LaRoche and her team have obtained the genomic sequences of microbes they have collected on ocean expeditions around the world and close to home in places such as the Bedford Basin and the Scotian Shelf. The sequences are entered into a huge database where they are analysed in the context of other oceanographic observations. As the observations accumulate over several years, the initial sequence information will serve as reference in the study the long term effects of climate change on life on Earth. “While we are discovering the roles of the microbes that live in the North West Atlantic waters, we are also establishing a baseline for comparing with the observations obtained in future studies, and assess what changes have taken place in the microbial population as a result of climate change.” Studying microbes means dealing with huge numbers. First, there are approximately 5 x 1030 microbial cells on earth representing an estimated 100 million species. The database that LaRoche and her team are working with is also huge; some 20 million sequences to date with four to five million pieces in each data set. “These are big files that take up a lot of memory. We can’t do it on a normal computer so we have to use ACENET.” LaRoche and her team have already compiled and analysed three and a half years of data using the ACENET system. The work is enabling scientists to understand the ways the world’s oceans – and life on Earth – are changing. “As the oceans continue to warm and to become more acidic, the microbial life within it may migrate closer to the poles in response,” she says. “This may affect the entire biome of the sea and that is why we need to study it.”