Biology

Animal populations living in North American cities are likely to undergo a significant shift as changes to the Earth’s climate intensify – and that, in turn, is likely to have an impact on us.

That is among the key findings of a University of Toronto study led by Alessandro Filazzola, who was recently a post-doctoral researcher in U of T Mississauga’s Centre for Urban Environments (CUE), a transdisciplinary research centre focused on promoting healthy urban environments.

Alessandro Filazzola (supplied image)

Filazzola used computer modelling to project the impact of global warming on more than 2,000 terrestrial animal species in the 60 most populated cities in Canada and the United States. He made predictions according to three different scenarios of greenhouse gas emissions and urban land use.

Published recently in the journal PLOS One, the study shows that across all three scenarios each of the 60 cities will experience both substantial gains and losses of urban species by the end of this century. In Toronto, for example, 40 to 195 species that currently live in Canada’s largest city are predicted to disappear, while 159 to 360 new species could emerge.

“Most Canadians live in cities, and the nature we interact with every day is in our backyard or local park,” says Filazzola, who has a PhD in biology and works as a data scientist focused on conserving biodiversity.

“The whole sea change in the assemblage of animals that live in our cities will have a large impact on how we behave in our day-to-day activities and what we value.”

Filazzola conducted the research with Marc Johnson, a professor of biology at U of T Mississauga and former director of CUE. His work was also supervised by Scott MacIvor, an associate professor of biological sciences.

To gather data on animal species, the researchers – who engaged leaders from Credit Valley Conservation, Conservation Halton and the Toronto and Region Conservation Authority to understand their top concerns in managing biodiversity – turned to the Global Biodiversity Information Facility, a free public resource featuring data about all types of life on Earth.

They modelled the historic and future distributions of 2,019 land-based animals in highly developed cities – 13 in Canada and 47 in the U.S. – with more than 400,000 residents. The computer modelling projections were shaped in part by bioclimactically relevant historical variables for each city, including average monthly minimum and maximum temperatures, and monthly precipitation.

The results predicted the highest introduction of new species in temperate cities – Quebec City and Ottawa in Canada, and Omaha and Kansas City in the U.S. Midwest. The largest declines in species are projected to take place in the subtropical parts of the U.S. and coastal California. Cities in arid parts of the U.S. – including Las Vegas, and Mesa and Tucson in Arizona – are expected to experience the fewest changes in species richness.

Meanwhile, cities that have historically experienced colder temperatures are predicted to have significantly higher gains in novel species and fewer losses in resident species. Urban areas with historically high precipitation were projected to have the highest species turnover – both the greatest gains and the largest losses. In the scenario with more intense development and greenhouse gas emissions, cities would experience significantly more species lost and gained.

The urban animals expected to be most negatively affected by climate change are amphibians, canines and loons.

“When the modelling predicts a big spike in temperature or a big drop in precipitation, you get a unique climate, and some species can endure it and some cannot – these are the ones that are probably going to be the most impacted and most likely to be lost,” Filazzola says.

The study notes that as urban ecosystems continue to transform due to global warming, shifts in our urban wildlife will have implications for our cultural identity and heritage – given how much animals figure into our national symbols and sports teams, the researchers say – and even our mental health.

“We know that having more green space and natural areas around us is very important for our well-being,” Johnson says. “If we lose nature, and the animals associated with it, it can negatively affect our psychological health.”

U of T researcher discovers critically endangered bats in two new locations

Christopher.Sorensen — Tue, 23 Jan 2024 21:56:26 +0000

U of T researcher discovers critically endangered bats in two new locations

Christopher.Sorensen Tue, 01/23/2024 - 16:56

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Finding the Jamaican flower bat in two new locations is raising hope for the critically endangered species (photo by Sherri and Brock Fenton)

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PhD student Phillip Oelbaum says finding new breeding grounds for the Jamaican flower bat raises hope for its survival and conservation

The Jamaican flower bat is endangered – so much so that experts believed only a small colony of about 500 existed in a single cave.

But an international team of researchers, including a PhD student from the University of Toronto Scarborough, recently discovered two new locations where the bat lives.

Published in Oryx, the International Journal of Conservation, the research shows the bat living in Jamaica’s Green Grotto Caves and Rock Spring Caverns.

“It’s exciting that we found them in two new locations, but it doesn’t mean they still aren’t in danger of going extinct,” says Phillip Oelbaum, a PhD student in Associate Professor Ken Welch’s lab in the department of biological sciences and lead author of the study.

“It also doesn’t mean they should be delisted as a critically endangered species. It just shows how little we know about them and that more research is needed.”

Nobody knows why, exactly, there are so few Jamaican flower bats in existence. The bat is found only in Jamaica so it’s possible its numbers may have always been low. It may also be threatened due to habitat disturbance from bauxite mining, predation from cats and guano harvesting. Guano (bat feces) is a highly sought after fertilizer because of its high nitrogen and phosphorus content and is commonly used by farmers growing cannabis.

The species was declared extinct until 2010 when a small colony was found in Stony Hill Cave, so finding these new breeding grounds raises hope for its survival and conservation, Oelbaum says.

A chance discovery

In Jamaica doing research on nectar and fruit-eating bats, Oelbaum says the Jamaican flower bat was on his radar, but he didn’t have high hopes of finding them.

The first location, Green Grotto Cave, is a popular tourist destination on the north part of the island just outside Runaway Bay. The bats were discovered in a lower part of the cave system in what’s known as the wild caves, a spot that’s not accessible to tourists. Previous acoustic detection and photos hinted that Jamaican flower bats might live there, but finding pregnant females was definitely a “happy accident,” says Oelbaum.

He almost didn’t make it to Rock Spring, the second spot, located in St. Mary Parish in the north, central part of the Island. The van Oelbaum was travelling in with fellow researcher Ronnie Hall, a grad student at the University of California, Merced, and Stefan Stewart, an expat Canadian and experienced cave explorer with the Jamaican Caves Organisation, hit a series of deep potholes and nearly rolled down the side of a hill.

“It was a rough start, and if it wasn’t for the help of local residents at Rock Spring who helped us get back on the road, we wouldn’t have made it to the cave at all,” Oelbaum says.

Oelbaum, a PhD student at U of T Scarborough, was in Jamaica doing research on fruit- and nectar-eating bats when he discovered Jamaican flower bats living in two previously unknown locations (photo by Don Campbell)

Despite arriving at their destination late, they took Stewart’s advice and set their harp traps next to a giant sinkhole known as Big Hole. A harp trap is a device that uses a series of strings to disrupt a bat’s flight, letting them drop harmlessly into a collection chamber.

As the sky grew darker a large funnel of bats emerged from the cave in what Oelbaum describes as a “batnado,” and once the bats flew into the trap it was just a matter of picking them up to check the species. That’s when they came across a lot of Jamaican flower bats.

What distinguishes the Jamaican flower bat is a bright pink forearm and the fur found on its upper body is often blondish and short compared to the buffy flower bat, which it closely resembles. It also has a protruding bone (known as a calcar) found on the inner side of the ankle.

“Even their facial structure is unique. Once you have one in your hand, there’s no mistaking it’s a Jamaican flower bat,” says Oelbaum.

Damion Whyte, Phillip Oelbaum and Ronnie Hall are currently doing bat surveys at sites across Jamaica (supplied image)

Next steps

Oelbaum is currently in Jamaica doing a survey of 30 locations with Damion Whyte, a PhD student at the University of the West Indies who was also an author on the study. They want to see if the Jamaican flower bat can be found at other locations.

The goal is to further study their habitat and behaviour since the bat is likely an important pollinator, and might also play a role in insect control and dispersing flower seeds. They also want to analyze hair and skin samples to better understand its diet.

“Damion is from Jamaica and has been instrumental in this research,” says Oelbaum. “I’m excited to see what else we can come up with and hopefully shed more light on this elusive bat.”

U of T biologist explains why there were so many mosquitoes this year

Christopher.Sorensen — Thu, 21 Sep 2023 16:50:27 +0000

U of T biologist explains why there were so many mosquitoes this year

Christopher.Sorensen Thu, 09/21/2023 - 12:50

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(photo by Jimmy Chan/Pexels)

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Mosquitoes hibernate over the winter and emerge to lay their eggs in stagnant pools of water as the temperature approaches 15 C

If you think there were more mosquitoes this year than usual, you’re not wrong.

Spring and summer in 2023 saw record temperatures across the globe, including in southern Ontario. Combined with a wetter-than-average season, that meant mosquitoes had more habitats in which they could reproduce and grow.

“It’s been extremely wet,” says Rosalind Murray, an assistant professor of biology at the University of Toronto Mississauga who studies insects. “That’s one of the main reasons we saw so many mosquitoes early on in the season.”

Mosquitoes, which hibernate over the winter, emerge to lay their eggs – usually in stagnant pools of water – as the temperature approaches 15 C.

And this year’s conditions were ideal: A warm spell in April melted lingering snow from the winter and was followed by heavy precipitation in May and June. That, in turn, created more habitat options for the insects to breed – including puddles in urban areas.

Rosalind Murray is an assistant professor of biology at U of T Mississauga (supplied image)

“As soon as it gets warm, they fly out of their hibernation areas and lay eggs wherever they can ... like parking lots or flooded lawns,” Murray says. “Mosquitoes are hardy – they can often survive in these puddles of water.”

If temperatures don’t cool off at night between warm spells – as was the case this spring – then mosquitoes have ideal conditions to proliferate. Warmer temperatures also increase the number of bacteria found in puddles, which mosquitoes eat.

And the warmer the temperatures, the faster mosquitos hatch. At 10 C, mosquitoes can grow from egg to adult in around 40 days, while in temperatures higher than 25 C, it takes just four days for mosquitoes to grow to adulthood. Depending on the species, mosquitoes live for a few days or a few weeks.

“There’s huge turnover of these animals, especially if we have wet and warm conditions where there’s a lot of habitats for them,” Murray says. “Their metabolism speeds up because it’s so warm.”

Climate change is exacerbating the wet and warm conditions favoured by mosquitos, bringing higher temperatures and more energetic weather systems. A growing concern is that southern species of mosquitoes are migrating to northern latitudes, serving as vectors for dengue fever, West Nile virus or the Zika virus.

“We are seeing more and more of these tropical species moving north,” Murray says.

One of Murray’s graduate students, Sherry Du, studies sexual dimorphism in mosquitoes. Du’s research reveals that mosquitoes are showing an affinity for puddles containing high concentrations of road salts.

“Mosquitoes have been found to love those environments,” Du says. “Urban or city mosquitoes are tough and hardy – they can tolerate polluted water conditions.”

Salty environments, meanwhile, place stress on dragonflies, which prey on mosquitoes. That means more mosquitoes survive because fewer are being eaten.

While warming temperatures could result in more mosquitoes than normal, it’s not a given. A dry season could negatively affect mosquito populations by limiting their habitat, Murray says.

As expected, mosquito populations began to dwindle in September and into the fall as they return to hibernation.

“But if we have a huge heat wave, then they’re going to come out,” Murray says.

U of T marine biologist dives deep in pursuit of ocean conservation data

Christopher.Sorensen — Thu, 14 Sep 2023 13:50:07 +0000

U of T marine biologist dives deep in pursuit of ocean conservation data

Christopher.Sorensen Thu, 09/14/2023 - 09:50

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U of T Mississauga Assistant Professor Cassidy D’Aloia, right, and PhD student Taylor Naaykens, left, take a selfie underwater after completing a successful field season (photo by Cassidy D’Aloia)

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Cassidy D’Aloia studies the population impact of larvae that travel far from their place of birth via ocean currents

Cassidy D’Aloia dives deep to learn about life under the sea, yielding critical data and research for marine conservation efforts.

An assistant professor of biology at the University of Toronto Mississauga, D’Aloia studies the molecular ecology of coastal fishes and invertebrates and tries to understand the patterns, causes and consequences of dispersal and gene flow in the ocean.

Put simply, she tries to understand where the offspring of sea organisms wind up – whether fish, molluscs or echinoderms – and how larvae move around in ocean currents.

“Do you eat fish? Do you want to keep eating fish? Then dispersal data is important if you want to predict how fish populations will fare for the future,” says D’Aloia, who joined U of T Mississauga last year after completing her postdoctoral work.

As part of her research, she runs the D’Aloia Lab, where she and a team of graduate students work at the intersection of marine ecology, evolution and conservation biology, asking many interdisciplinary questions with answers that have profound implications for the future of marine life and conservation efforts.

D’Aloia examines the sea floor on the hunt for fish (photo by Taylor Naaykens)

Scuba diving in the coral reefs

D’Aloia and her team often collect ocean life data by scuba diving. Dives have taken place in the southern Caribbean Sea off the coast of Belize or Curaçao, or in the North Atlantic off the coast of eastern Canada. Because much of their field work focuses on organisms living in coral reefs, they see firsthand the effects of climate change on the health of these ecosystems.

Diving off the coast of Belize this past summer, D’Aloia says she saw how damaged coral reefs have become.

“Corals are critical to marine biodiversity,” she says. “Rising ocean temperatures are a huge problem for coral reefs because of the impact. We study a lot of things that live on corals and this year the coral bleaching was bad.”

Coral bleaching happens when the water becomes too warm and corals expel algae living in their tissues, causing them to turn completely white. While the bleaching doesn’t necessarily kill the corals, it places them under more stress and makes them vulnerable to disease. That, in turn, can impact other species that are dependent on them, including humans that rely on the ocean for their livelihoods.

A healthy reef with high cover of living coral off the coast of Curaçao (photo by Cassidy D’Aloia)

An average day in the field in Belize involves waking up at 6 a.m. to eat breakfast and ready the scuba equipment before getting to the water by 8 a.m. From there, D’Aloia and her team swim out to the coral reef and begin diving where they record data, map populations and collect tissue samples from tiny organisms for genetic analysis.

With a few breaks in between, the team makes deep dives three times a day before heading back to the field station by 4 p.m. to clean the gear, back up data, make dinner and sleep. The field work goes on six days a week for a month or two.

“Our field work is gruelling,” D’Aloia says. “But I just love it. Being in the field is by far the best part of the job. It’s a very special feeling being underwater – like visiting another planet. It’s a real privilege to be able to do that.”

D'Aloia has worked in Belize for many years, building and strengthening relationships with local fishers, the University of Belize and other researchers. Her work has led to several partnerships, including Fisheries and Oceans Canada. She works with the federal government department to develop science-based management plans for Canada’s fish stocks.

D’Aloia’s current research in Belize is funded by the Belize Fund for a Sustainable Future and U of T Mississauga, in collaboration with the University of Belize’s Environmental Research Institute.

A coral-dwelling fish (Elacatinus evelynae) sitting atop a healthy coral (photo by Cassidy D’Aloia)

The importance of data

To understand how larval development of marine life is connected to conservation efforts, D’Aloia explores the consequences of larvae travelling far from their place of birth on ocean currents.

“We’re interested in how organisms move in the very early part of their life cycle,” she says. “It sounds simple, but it’s a tricky problem in marine biology.”

Larval dispersal determines how populations change over time and how they evolve. Species studied include snails, gastropods, cod, American lobster, sea cucumbers, hogfish and conch fish.

“Fish and harvested invertebrates are one of the last wild animals we still harvest in their natural environment, so I think it lends itself well to the integration of science and policy and trying to work together to give the fundamental scientific data that can help us make sustainable choices,” D’Aloia says.

“If we want to make decisions on spatial conservation, then you need this data.”

D’Aloia grew up in New York state, away from the ocean, but says she always loved science and biology. As a result of great high school teachers and encouraging university professors, she sought to become a marine biologist and “fell in love with the ocean.”

PhD student Taylor Naaykens runs surveys and counts fish underwater (photo by Cassidy D’Aloia)

Now an assistant professor overseeing a team of graduate students, she offers training and support for students to conduct research and build their careers as marine biologists. That includes learning how to scuba dive.

“Research that can support the conservation of those ecosystems is so important,” D’Aloia says. “I think supporting students who are trying to pursue good research and want to make a difference in the world is a good thing.”

‘Fascinating, gruesome, counterintuitive’: U of T profs explore bug sex on CBC's The Nature of Things

bresgead — Tue, 14 Mar 2023 15:14:47 +0000

‘Fascinating, gruesome, counterintuitive’: U of T profs explore bug sex on CBC's The Nature of Things

bresgead Tue, 03/14/2023 - 11:14

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U of T Scarborough biology professors Maydianne Andrade and Andrew Mason took part in a recent episode of The Nature of Things that explored bug sex (photo courtesy of Andrew Gregg/Red Trillium Films)

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As the most numerous animals on Earth, there’s no doubt that bugs have been getting busy.

Several University of Toronto researchers recently shared their insights into insects’ mating rituals in the Bug Sex episode of The Nature of Things, a CBC documentary series hosted by environmentalist David Suzuki.

“Sex in bugs is fascinating, gruesome, counterintuitive,” says Maydianne Andrade, professor in the department of biological science at U of T Scarborough and renowned expert on the mating habits of cannibalistic spiders.

“It’s ridiculous in its complexity. Ridiculous in how extreme it is, and most people know nothing about it.”

Andrade, who came up with the original concept for the documentary and was the story editor, appeared in the documentary alongside U of T Scarborough colleague Andrew Mason, a professor and chair of the department of biological sciences who studies bug acoustics and behaviour. Catherine Scott, who completed her PhD under Andrade at U of T Scarborough and is currently a post-doctoral researcher at McGill University, also took part in the documentary.

They were joined on the episode by U of T Mississauga’s Darryl Gwynne, a professor emeritus of biology, and Rosalind Murray, an assistant professor of biology.

“Nature is amazing in what it generates in terms of diversity – same thing goes for the mating game,” says Gwynne, who was Andrade’s PhD supervisor.

After the episode premiered on CBC’s streamer, Murray appeared on Fresh Air on CBC Radio to discuss her research into the sexual activity of an Ontario species of dance flies.

Watch the episode on CBC's The Nature of Things

Most species evolve by adapting to similar, large-scale environmental pressures, study finds

lanthierj — Mon, 02 Jan 2023 12:45:44 +0000

Most species evolve by adapting to similar, large-scale environmental pressures, study finds

lanthierj Mon, 01/02/2023 - 07:45

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The Amazonian bird Lepidothrix natererei, better known as the snow-capped manakin, and its close relative were among 3,000 pairs of animals studied (photo by Maya Faccio).

Alexa Battler

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Breaking Research

Department of Biological Sciences

Biology

Research & Innovation

U of T Scarborough

Since the days of Charles Darwin, evolutionary biologists have widely believed that most new species form because they’ve adapted to different environments – but a new University of Toronto study suggests otherwise.

The study, published in the journal Science, sheds light on what researchers have dubbed a “blind spot” in our understanding of why new species form.

“We found species are actually consistently adapting to similar environmental pressures,” says Sean Anderson, who co-authored the paper with Professor Jason Weir while earning his PhD at U of T Scarborough. “They're undergoing classic Darwinian adaptation, but they're not doing it in very different environments.”

While it’s generally agreed that populations must be physically separated to begin evolving into new species, researchers say what happens during that isolation has been murky. For decades the prevailing theory has been ecological speciation – that groups evolve because they migrate to different environments and experience pressures the rest of their species don’t face, be it new food sources or predators. Called divergent adaptation, environmental features then drive the natural selection that causes a new species to form. Darwin’s finches, which developed beaks that were better suited for seeds than they were insects, are one example.

Sean Anderson defended his PhD in May while working with Jason Weir at U of T Scarborough (Submitted photo).

But it’s also common to see species that have evolved to the point they can no longer breed with their closest relatives, yet still share most of the same traits as their counterparts. That gave researchers the hunch that the environments in which evolution took place, though geographically distant, may not have been so distinct. It’s an established but less embraced explanation known as parallel adaptation.

“Ideas of divergent adaptation have been dominated to a considerable extent by the study of model organisms – the species that have these great ecological differences,” Anderson says. “We wanted to see what patterns we could find by studying as many species as possible.”

The researchers used the largest and broadest dataset of divergent traits found in species and their closest relatives – called sister pairs – ever assembled. They also created a statistical model that can, for the first time, estimate whether a species evolved under parallel or divergent adaptation. Across almost 3,000 sister pairs of birds, mammals and amphibians, species overwhelmingly evolved under similar large-scale environmental pressures.

“We found this really consistent signature where parallel adaptation seems to be what dominates – and it doesn't matter what traits you look at, it's the same in just about every group of species pairs you've got,” says Anderson, who is now completing post-doctoral research at the University of North Carolina at Chapel Hill. “We were surprised at just how consistent this signature was.”

Lepidothrix iris (left) and Lepidothrix natererei (right), two species of manakin, descended from populations that began to evolve in separate environments (photo by Maya Faccio).

Anderson says that, in some cases, species may be evolving similar traits while undergoing changes at the genetic level. That can lead them to become different species.

“It's often not just one pressure – species are facing a whole collection of pressures that are similar,” Anderson says. “And the external environment is not the only thing that can throw challenges at a species. Its own genome can do that by producing things like selfish genetic elements.”

The results could have far-reaching implications since theories about what causes species to evolve help biologists draw conclusions about biodiversity. If most species evolve under divergent adaptation, building biodiversity requires diverse habitats with different resources and challenges. But if it’s parallel adaptation, biodiversity depends on geographic distance and time apart.

“The impact I hope this will have is that people will not assume necessarily that divergent adaptation drives speciation,” Anderson says. “These results might also change the way we look at how biodiversity evolves, and the factors that we think are most important.”

Drone-based technology remotely assesses health of trees impacted by climate change

Christopher.Sorensen — Tue, 24 May 2022 16:54:40 +0000

Drone-based technology remotely assesses health of trees impacted by climate change

Christopher.Sorensen Tue, 05/24/2022 - 12:54

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The Ensminger Lab's drone flight team has developed a technology that remotely assesses photosynthetic phenology and plant fitness (photo courtesy of Ensminger Lab)

Topic

Research and Innovation

Sustainability

U of T Mississauga

Canada has nearly 362 million hectares of forest, but climate change is negatively impacting tree health and productivity. Trees planted today need to withstand future climate instability.

Enter Ingo Ensminger, an associate professor of biology at the University of Toronto Mississauga, and an innovative new technology that could provide further insights into tree health. Ensminger’s lab studies plant-environment interactions and the impact of climate change on metabolism and photosynthesis of plants from molecular to leaf, species and ecosystem level.

Ingo Ensminger

Ensminger and his team have developed a drone-based technology, dubbed the FastPheno project, that remotely assesses photosynthetic phenology and plant fitness.

“Most people who use drones in trees and forests try to measure height and the size of the canopy, they use drones for inventories,” he says. “Our goal is different – we try to assess health and fitness, and overall performance as indicated by the ability of vegetation to remove CO2 from the atmosphere when they photosynthesize and produce biomass.”

Ensminger was recently awarded $4.7 million in funding for his FastPheno project by Genome Canada, an independent, federally funded not-for-profit.

“It is very rewarding to receive funding to develop and implement tools that will hopefully be used to help tree breeders and forest practitioners to identify trees that are resilient to climate change,” says Ensminger, who anticipates the tools will be used for tree improvement programs or to set targets for forest conservation and management.

Genome Canada’s Genomic Applications Partnership Program brings new applied genomics solutions to issues facing Canadians, and supports collaborations in forestry and other sectors.

The unique technology enables them to distinguish the performance of thousands of trees, and researchers can use the approach to detect drought stress control on photosynthesis in natural forests.

“All this is based on the optical fingerprint of vegetation,” Ensminger explains. “This fingerprint is derived by measurements of leaf spectral reflectance. Leaf spectral reflectance is highly variable, and it can be used as a plant health indicator, because it changes upon exposure to drought stress or heat stress.” The fingerprint is also species-specific, and hence future work in Ensminger’s lab will also explore how species can be distinguished to monitor biodiversity.

When it comes to tree breeding and forest conservation, the ability to distinguish trees that perform well during drought and heat is incredibly useful — complementing genomic selection with adaptive traits could help produce trees resilient to future climate in Canada.

Simply put, Ensminger believes, it could transform Canada's forest sector.

“Outcomes have been very promising,” Ensminger reports. “We can distinguish trees that are water-stressed from well-watered trees, we can assess how photosynthetic activity varies over the course of the year, and in large forest stands we can identify trees that perform well and distinguish those from unhealthy trees or trees that are stressed.”

Ensminger’s technology is fast, reliable and cost-effective compared to vegetation monitoring that relies on visual inspections and manual measurements. New research enabled through FastPheno now aims to apply the drone-based phenotyping approach at a large scale and explore how reliably it can be used across forests in Ontario and Quebec to monitor the health and fitness of individual trees.

If successful, FastPheno could create cost savings of $540 million per year and reduce assessment times from a matter of weeks to hours – and it can be transferred from forest vegetation to applications in agriculture, conservation and biodiversity studies.

St. Casimir experimental forest in Quebec, a field site where Ensminger and his team do a lot of their drone work (photo courtesy of Éric Dussault, Natural Resources Canada)

What’s next for Ensminger’s team? During their drone flights, they’re collecting an enormous amount of data – and now it’s a matter of processing and analyzing it. They’re collaborating with robotics experts to improve field data collection and will be developing tools to automate the process of image analysis and pixel classification using machine learning and AI technologies.

“We also aim to develop software and web-interfaces that provide users access so that not just researchers, but a wide range of end-users have access to the data produced through this approach,” he says.

“This is an exhilarating time for genomics,” noted Rob Annan, Genome Canada President and CEO, following a federal announcement of funding in March for FastPheno and other projects. “The knowledge, tools and technologies it is generating are driving innovation in traditional sectors and helping them achieve green growth, as well as improving the health and quality of life of Canadians.”

Ensminger’s project will complement the genomic selection research and operational programs of Natural Resources Canada and the Ministry of Forests, Wildlife and Parks of Quebec.

U of T researcher reveals new insights on link between genetic mutations and biological evolution

Christopher.Sorensen — Wed, 18 May 2022 19:33:46 +0000

U of T researcher reveals new insights on link between genetic mutations and biological evolution

Christopher.Sorensen Wed, 05/18/2022 - 15:33

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An abstract illustration of experiments carried out at U of T Mississauga that show how different combinations of genetic mutations can have an impact on the evolutionary process (illustration by Alex N. Nguyen Ba)

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Research & Innovation

U of T Mississauga

From the longer-beaked Galapagos Island finches studied by biologist Charles Darwin – which enabled them to more effectively snatch insects – to the ability of some humans over others to digest milk, genetic differences that give organisms a competitive edge drive the process of natural selection.

Now, research by Alex N. Nguyen Ba, an assistant professor of biology at the University of Toronto Mississauga, adds an important dimension to our understanding of how genes interact in the evolutionary process.

Alex N. Nguyen Ba

He is the co-principal investigator of a first-of-its-kind study, published this month in the journal Science, that shows different combinations of genetic mutations can have an impact on the evolutionary process – a finding that could benefit areas such as personalized medicine and vaccine design.

“Evolution is a force that drives all of life on this planet,” Nguyen Ba says. “Understanding how much we can predict about adaptation has been of strong interest to many people in the field.”

He compares adaptation to climbing a mountain. There are several possible routes to the peak – each with its own specific terrain to negotiate. So, how can scientists predict the route to the mountain top?

“There are huge implications if we can figure out what’s going to happen in the future for living organisms,” he says.

At U of T Mississauga’s annb lab, Nguyen Ba and his team of researchers explore genetic mutations in cells and their impact on evolution using next-generation technologies. These include high-throughput synthetic biology – designing new biological systems or changing existing ones for research purposes – and a desk-sized robot that can process numerous biological samples.

He began the study five years ago when he was a post-doctoral researcher at Harvard University’s Desai Lab. There, he collaborated with Christopher Bakerlee, who is the study’s co-principal investigator.

Together, Nguyen Ba and Bakerlee used CRISPR gene-editing technology to alter genes in the cells of yeast, which is commonly used in genetic engineering research because it shares some genes with humans.

They worked with 10 missense mutations, which are aberrations in DNA code that change the production of amino acids. Considered the building blocks of life, amino acids are molecules that combine to form proteins, which help with everything from healing wounds to providing energy and making antibodies.

The experimentation process involved testing out all possible combinations of these mutations – 1,024 in total. The scientists wanted to determine how interactions between genes affect the expression of certain genetic traits.

Nguyen Ba completed the final year of the study at U of T Mississauga, where he analyzed and interpreted the data. The study revealed that evolution frequently samples combinations of gene mutations with negative synergy between them. This acts on the yeast’s evolutionary potential in negative ways, for example, by slowing their rate of adaptation.

The findings run counter to the commonly held belief that all biological adaptation unfolds in a predictable way due to some unknown biological law.

Instead, combinations of mutations that have accumulated through time dictate the future evolutionary potential of an organism.

Moreover, he says, it challenges the dominant view in genetic research that we should study one gene mutation at a time. Instead, examining mutations in combination could help us understand diseases and lead to more precise medicine.

“We're showing that in order for us to have a full understanding of how genes actually behave, the combinations of mutations are likely to be very important.”

Urbanization is driving the evolution of plants around the world, U of T study finds

Christopher.Sorensen — Thu, 17 Mar 2022 19:18:45 +0000

Urbanization is driving the evolution of plants around the world, U of T study finds

Christopher.Sorensen Thu, 03/17/2022 - 15:18

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A study led by U of T researchers had scientists from around the world examine white clover since it's present in almost every city on Earth and provides a tool to understand how urban environments influence evolution (photo by Nick Iwanyshyn)

Topic

Research & Innovation

U of T Mississauga

Humans are constantly re-shaping the environment by building sprawling cities, but a new study demonstrates that urban environments are also altering the way life itself evolves – and it’s happening all around the world.

Researchers, led by evolutionary biologists at the University of Toronto Mississauga, analyzed data about the white clover plant that was collected by 287 scientists in 160 cities across 26 countries, from Toronto and Tokyo to Melbourne and Munich. They found the clearest evidence yet that humans in general, and cities specifically, are a dominant force driving the evolution of life globally – with white clover frequently evolving in direct response to environmental changes taking place in urban settings.

The results of the Global Urban Evolution Project (GLUE) were published this week in the journal Science.

“We’ve long known that we’ve changed cities in pretty profound ways and we’ve dramatically altered the environment and ecosystems,” says study co-lead James Santangelo, a PhD student in biology at U of T Mississauga. “But we just showed [the reverse] happens, often in similar ways, on a global scale.”

The GLUE study illustrates that the environmental conditions in cities tend to be more similar to each other than to nearby rural habitats. In that sense, downtown Toronto is more comparable to downtown Tokyo than it is to surrounding farmland and forests outside of the city.

Not only were researchers able to observe global adaptation to cities, they identified the genetic basis of that adaptation and the environmental drivers of evolution. White clover produces hydrogen cyanide as both a defense mechanism against herbivores and to increase its tolerance to water stress, and GLUE found that clover growing in cities typically produce less of it than clover in neighbouring rural areas due to repeated adaptation to urban environments.

The changes in the presence of herbivores and water stress in cities are pushing white clover to adapt differently than their rural counterparts – a finding that holds true for cities across various climates and which holds implications that reach far beyond the humble clover plant.

James Santangelo, a PhD student in biology at U of T Mississauga, co-led the study, which analyzed data about the white clover plant that was collected by 287 scientists in 160 cities across 26 countries (photo by Nick Iwanyshyn)

“This study is a model to understand how humans change the evolution of life around us,” says Rob Ness, an assistant professor of biology at U of T Mississauga who co-led the project with Santangelo and Professor Marc Johnson. “Cities are where people live and this is the most compelling evidence we have that we are altering the evolution of life in them.

“Beyond ecologists and evolutionary biologists, this is going to be important for society.”

GLUE examined white clover because it is one of the few organisms present in almost every city on Earth, providing a tool to understand how urban environments influence evolution.

Johnson says now that we know humans are driving evolution in cities across the planet, the information can be used to start developing strategies to better conserve rare species and allow them to adapt to urban environments. It can also help us better understand how to prevent unwanted pests and diseases from adapting to human environments, he says.

For GLUE, this study is just the beginning. Using the same techniques, collaborators collected more than 110,000 clover samples from 160 cities and nearby rural areas and have sequenced more than 2,500 clover genomes, creating a massive dataset that will be studied for years to come.

The unprecedented global collaboration began with a single tweet.

“Nearly everyone we asked to collaborate said yes – and that was kind of remarkable, because we were asking people to take on a lot of work,” says Johnson, who co-ordinated the more than 280 other researchers who participated in the study. “Our collaborators recognized the importance of this project. There has never been a field study of evolution of this scale, or a global study of how urbanization influences evolution.

"It would have been impossible to do this without our global set of collaborators.”

Johnson calls the project a model for inclusive science since team was equally split between women and men, and included not just established researchers, but also students at all levels and from all inhabited continents around the world.

Correcting the fossil record: Researchers say four-legged ‘snake’ is different ancient animal

Christopher.Sorensen — Thu, 06 Jan 2022 20:34:24 +0000

Correcting the fossil record: Researchers say four-legged ‘snake’ is different ancient animal

Christopher.Sorensen Thu, 01/06/2022 - 15:34

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(Photo by kristianbell/Getty Images)

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It all started with a grand claim: scientists had discovered the first known four-legged snake fossil from Brazil. The specimen, named Tetrapodophis amplectus, was small – about the size of a pencil – with tiny limbs. It was considered a significant discovery that offered paleontologists a major clue into the transition from limbed lizards to limbless snakes.

But the interpretation of this latest discovery didn’t sit well with University of Toronto’s Robert Reisz, a professor of biology at U of T Mississauga, and his colleagues – so he and Michael Caldwell, a professor of biological sciences at the University of Alberta, went to study the fossil in person.

“We came up with a much more plausible alternative explanation that this is not a snake, but a little lizard,” Reisz says.

Reisz adds the way in which the fossil was first obtained raised red flags. Around the mid-20th century, Brazil had outlawed fossil exports – but this artifact was illegally exported and bought by a private collector.

“It was quite unethical,” he says. “There are laws in place now to protect (these national treasures) and we should respect those and work within the system rather than be tempted by the attraction of an exciting fossil you get through unethical means.”

Fossil of Tetrapodophis amplectus (photo supplied by Robert Reisz)

Reisz and Caldwell went to Germany to look over the fossil, which was housed in a small, private museum that exhibits materials from the region, including Jurassic reptiles and dinosaurs.

“We re-studied it, spent a couple days with it, and found that the available evidence was much better than was originally presented ... because in addition to the actual fossil, there was also extensive impression,” Reisz says, adding that he and Caldwell got a lot of information from the impression of the specimen’s skull.

He explains that when a fossil forms between layers of rock, the impression it creates as it becomes rock, together with sediments, is extremely valuable because of its precision.

In this case, the rock that the fossil was extracted from was split – with the skeleton and skull on opposite sides of the slab. The shape of each was preserved as an impression on the opposite side. The original study overlooked the natural impression that showed that the skull was “more lizard-like than snake-like,” Reisz says.

Reisz says snakes have an extremely mobile skull where many bones are reduced and others are loosely connected to each other – particularly around the back end of the skull and jaw joint. He adds that snakes can also move several bones out of the way, while still connected to each other in the skull, to swallow prey whole.

Reisz and Caldwell also discovered that the original authors’ claims about the arrangement of the specimen’s teeth were false.

He explains that a snake’s teeth are designed to allow prey to go in one direction down the mouth, but they are strongly curved to prevent any movement out of the mouth. “So not only was the skull more lizard-like than snake-like, but the teeth were more lizard-like too,” Reisz says.

While he and his colleagues found that the Tetrapodophis amplectus wasn’t a snake, Reisz says it’s still a significant fossil. The team found that the anatomy was consistent with the anatomy of dolichosaurs – an group of extinct marine lizards from the Cretaceous period. It shows yet another example of the way lizards evolved and reduced their limbs to adapt to their environment, he says.

Reisz adds that the story also serves as a reminder that “science is a quest for truth, and the closer we get to the truth, the better.”

“We want to find out, and get as close to, the truth as possible,” he says. “Every time we find yet another interesting fossil, it gets us closer to that. We find out more about life before us.”

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