Evolution

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

Cutline

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)

Sharon Aschaiek

Topic

Breaking Research

Biology

Evolution

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 ��Ƶ 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.”

Increases in rats, bedbugs and mosquitoes are unintended consequence of urbanization: U of T expert

rasbachn — Thu, 02 Nov 2017 16:53:11 +0000

Increases in rats, bedbugs and mosquitoes are unintended consequence of urbanization: U of T expert

rasbachn Thu, 11/02/2017 - 12:53

Cutline

“As we build cities, we have little understanding of how they are influencing organisms that live there,” says Marc Johnson, a director of the ��Ƶ’s Centre for Urban Environments (photo by Natalie Behring via Flickr)

Topic

Faculty of Arts & Science

Research & Innovation

��Ƶ Mississauga

The recent uproar about seats on a British Airways flight crawling with bedbugs is only one of the unintended consequences that urbanization worldwide has on evolution, says a ��Ƶ researcher whose new study takes a comprehensive look at those consequences.

“As we build cities, we have little understanding of how they are influencing organisms that live there,” says Marc Johnson, an associate professor of biology at U of T Mississauga who is also a director of the ��Ƶ’s Centre for Urban Environments.

“It’s good news that some organisms are able to adapt, such as native species that have important ecological functions in the environment. But it can also be bad news that the ability of some of these organisms to adapt to our cities might increase the transmission of disease. Bedbugs, for example, were scarce two decades ago, but they’ve adapted to the insecticides used to keep them at bay and have exploded in abundance worldwide.”

In the first study to take a broad look at the way urbanization is affecting evolution, Johnson (left) and Jason Munshi-South, an associate professor of biological sciences at Fordham University, reviewed all existing research studies about urbanization and evolution and synthesized the results.

“Traditionally, we’ve thought about evolution as a long-term process driven by environmental pressures and the interactions between species. But now there is a new driver that is rapidly changing many other species, which is how they interact with humans and our built environment," says Munshi-South. “Humans and our cities are one of the most dominant forces of contemporary evolution now.”

Interested in publicly funded research in Canada? Learn more at UofT’s #supportthereport advocacy campaign

The study raises questions about which native species can persist during urbanization and whether those that adapt will influence the health of ecosystems and human beings. Loss of habitat and urban barriers, such as roads and buildings, pose challenges to all kinds of species and some may adapt in undesirable ways. The researchers assessed various means of genetic adaptation, such as mutation, the movement of genes through dispersal, neutral evolution and adaptive evolution through Darwinian natural selection, concluding that the urban environment has an impact on each of these mechanisms of evolution.

Their work touches on mammals, plants, birds, amphibians, reptiles, insects and viruses, identifying evolutionary impacts on species as diverse as the common blackbird in Europe to white clovers and white-footed mice in North America. Populations of white-footed mice in New York City, for example, became differentiated from each other after urbanization, due to their isolation in various parks.

“We’ve created a novel ecosystem that no organism has ever seen before,” says Johnson, noting that their study, published in the journal Science, is a “wake-up call for the public, governments and other scientists.”

He and Munshi-South suggest that we need to think carefully about how we’re altering our environment when we build cities, influencing the evolution of species that may, in turn, influence our lives. A number of organisms, such as rats, urban lizards, cockroaches, pigeons and bedbugs, have evolved to depend on humans.

Read the study in the journal Science

There are now mosquitoes, for example, that have evolved to live in the London Underground stations and adapted so that they no longer need to feed on blood to produce eggs. They also have no need to become dormant during the winter. Unfortunately, these mosquitoes can carry a number of diseases and are now found in New York City, Chicago and Los Angeles, too. Our health-care systems may be required to adapt in response.

Johnson and Munshi-South suggest that when we’re planning cities, we need to think about the impact our designs have on native species and whether we can design them to “be kinder to ourselves and the environment,” considering ways to conserve native species and mitigate the prevalence of disease-carrying pests.

Given that species are evolving so rapidly in response to urbanization, the outdoors also becomes a classroom that offers an opportunity to see examples of evolution first-hand. Urban evolution can be used as a tool to educate city dwellers and others about the reality and importance of evolutionary biology.

“People who don’t believe in evolution need not go further than their backyards to see evidence of it,” Johnson says.

The study was funded by grants from the National Science Foundation and the Natural Sciences and Engineering Research Council of Canada.

Human ancestors originated in Europe – not Africa? U of T part of international team studying pre-human remains

ullahnor — Tue, 23 May 2017 16:47:59 +0000

Human ancestors originated in Europe – not Africa? U of T part of international team studying pre-human remains

ullahnor Tue, 05/23/2017 - 12:47

Cutline

El Graeco lived 7.2 million years ago in the dust-laden savannah of the Athens basin. This view is from El Graeco’s place of discovery, Pyrgos Vasilissis (painting by Chicago-based artist Veliza Simeonovski)

Sean Bettam

Author legacy

Sean Bettam

Topic

Global Lens

Evolution

Faculty of Arts & Science

Humans and chimpanzees split from their last common ancestor several hundred thousand years earlier than believed – and this occurred in Europe, not Africa – according to an international team of scientists.

��Ƶ’s David Begun, a paleoanthropologist in the Faculty of Arts & Science, is a co-author of one of two controversial studies reported today on the pre-human remains in PLOS ONE.

“Our discovery outlines a new scenario for the beginning of human history – the findings allow us to move the human-chimpanzee split into the Mediterranean area,” Begun said. “These research findings call into question one of the most dogmatic assertions in paleoanthropology since Charles Darwin, which is that the human lineage originated in Africa.

“It is not a matter of continental bragging rights. It is critical to know where the human lineage arose so that we can reconstruct the circumstances leading to our divergence from the common ancestor we share with chimpanzees. Not having this information is like having a crime without the crime scene.”

Researchers analyzed two known fossil specimens of Graecopithecus freybergi using state-of-the-art methods – a lower jaw from Greece and an upper premolar from Bulgaria – and came to the conclusion that they belong to pre-humans. Furthermore, Graecopithecus is several hundred thousand years older than the oldest potential pre-human from Africa, the six to seven-million-year-old Sahelanthropus from Chad.

Using computer tomography, they visualized the internal structures of the Graecopithecus fossils and demonstrated that the roots of premolars are widely fused. The lower jaw, nicknamed El Graeco by the scientists, has additional dental root features, suggesting that the species Graecopithecus freybergi might belong to the pre-human lineage.

“While great apes typically have two or three separate and diverging roots, the roots of Graecopithecus converge and are partially fused – a feature that is characteristic of modern humans, early humans and several pre-humans including Ardipithecus and Australopithecus,” said Madelaine Böhme from the Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, who co-led the investigations with Nikolai Spassov from the Bulgarian Academy of Sciences.

Read about the discovery in the Globe and Mail

Giant sperm give male worms a reproductive edge, U of T research reveals

lavende4 — Tue, 27 Sep 2016 14:46:13 +0000

Giant sperm give male worms a reproductive edge, U of T research reveals

lavende4 Tue, 09/27/2016 - 10:46

Cutline

Big questions remain, says U of T ecology and evolutionary biologist Asher Cutter (Photo by Diana Tyszko)

Peter Boisseau

Author legacy

Peter Boisseau

Topic

Breaking Research

Faculty of Arts & Science

Ecology & Evolutionary Biology

Some worms have taken the notion that “bigger is better” to extremes by evolving giant sperm cells that are up to a quarter the size of their own bodies, a study led by a ��Ƶ scientist and researchers in France has discovered.

While other male animals use everything from big antlers to seductive mating sounds, sperm gigantism is the strategy worms may favour, especially when facing strong competition for females, says the study by U of T ecology and evolutionary biologist Asher Cutter and colleagues Christian Braendle and Anne Vielle of the University of Nice.

“There are a lot of different ways that males in other species try to be successful in reproduction, which is why sometimes you have physical competitions between deer, or birds trying to attract a mate with a song,” says Cutter, an associate professor.

“And in other cases, as we see in these worms, it is a matter of competition after mating happens, and it’s actually the sperm cells that are competing against one another.”

The giant sperm move like an amoeba and have a ‘foot’ called a pseudopod to help them crawl around the female reproductive tract, seeking out the ovulating eggs. The bigger the sperm, the faster they crawl, and the better chance they have to fertilize an egg.

But being big does come at a cost, so at times the worm turns to another strategy that instead relies on quantity, producing lots of little sperm instead of a few big ones.

“We don’t know exactly what it is that is specifically driving the production of these very large sperm cells, and in what situations they are more likely,” says Cutter.

“One possible idea is that the much larger sperm cells are better at fertilizing the eggs in some species, but not in others. Another possibility is that these larger sperm are packed with some kind of energy reserves that actually help give the developing embryo the nutrition that it needs.”

It may also be that when the worms live in small mating groups, competition favors the evolution of large male sperm, but when there are a lot of females around, smaller sperm do a better job of inseminating as many of them as possible.

“The data seems to suggest that, but we’d really like to look at it further,” says Cutter. “The one thing we can say for certain about the science of giant sperm is that big questions remain.”

It’s not as if Earth could someday be facing an attack of the giant worm. Although the sperm cells are large, the worms studied were just one millimeter long, or about the thickness of a coin.

But the study of the 26 worm species published in the Aug. 26, 2016 issue of the journal Evolution provides the first insights into sperm size differences in Caenorhabditis nematodes.

And with scientists struggling to understand any number of current mysteries about the natural world, such as bees dying off and bird populations plummeting, new insights into the whys and wherefores of animal reproduction are a welcome addition to the research they can draw upon.

“It’s certainly the case that when you make a discovery in one area, people with expertise in another area sometimes have a light go off in their head, and see a connection that no one has seen before.”

Why we're smarter than chickens

sgupta — Fri, 21 Aug 2015 13:02:38 +0000

Why we're smarter than chickens sgupta Fri, 08/21/2015 - 09:02

Cutline

(photo by Johnathan Nightingale via Flickr)

Jovana Drinjakovic

Author legacy

Jovana Drinjakovic

Topic

Subheadline

Researchers at U of T’s Donnelly Centre uncover protein part that controls neuron development

U of T researchers have discovered that a single molecular event in our cells could hold the key to how we evolved to become the smartest creatures on the planet.

Professor Benjamin Blencowe and his team at the Donnelly Centre for Cellular and Biomolecular Research have determined that a small change in a protein called PTBP1 spurred the creation of neurons and fuelled the evolution of mammalian brains to become the largest and most complex among vertebrates.

The study is published in the August 20 issue of Science.

Brain size and complexity vary enormously across vertebrates, but it is not clear how these differences came about. Humans and frogs, for example, have been evolving separately for 350 million years and have very different brain abilities. Yet scientists have shown that they use a remarkably similar repertoire of genes to build organs in the body.

So how is it that a similar number of genes, which are also switched on or off in similar ways in diverse vertebrate species, generate a vast range of organ size and complexity?

The key lies in alternative splicing (AS), whereby gene products are assembled into proteins, which are the building blocks of life. During AS, gene fragments called exons are shuffled to make different protein shapes. It’s like LEGO, where some fragments can be missing from the final protein shape.

AS enables cells to make more than one protein from a single gene, so that the total number of different proteins in a cell greatly surpasses the number of available genes. A cell’s ability to regulate protein diversity at any given time reflects its ability to take on different roles in the body.

Blencowe’s previous work showed that AS prevalence increases with vertebrate complexity. So although the genes that make bodies of vertebrates might be similar, the proteins they give rise to are far more diverse in mammals than in birds and frogs.

And nowhere is AS more widespread than in the brain.

“We wanted to see if AS could drive morphological differences in the brains of different vertebrate species,” says graduate student Serge Gueroussov, lead author of the study. Gueroussov previously helped identify PTBP1 as a protein that takes on another form in mammals. The mammalian form of PTBP1 is shorter because a small fragment is omitted during AS and does not make it into the final protein shape.

Could this newly acquired, mammalian version of PTBP1 provide clues to how our brains evolved? PTBP1 is both a target and major regulator of AS. PTBP1’s job in a cell is to stop it from becoming a neuron by holding off AS of hundreds of other gene products.

Gueroussov showed that in mammalian cells, the presence of the shorter version of PTBP1 unleashes a cascade of AS events, tipping the scales of protein balance so that a cell becomes a neuron.

What’s more, when Gueroussov engineered chicken cells to make the shorter, mammalian-like PTBP1, this triggered AS events that are found in mammals.

“One interesting implication of our work is that this particular switch between the two versions of PTBP1 could have affected the timing of when neurons are made in the embryo in a way that creates differences in morphological complexity and brain size,” says Blencowe, who is also Banbury Chair in Medical Research and a professor in the department of molecular genetics.

(Image at right: frog and human brain, to scale.)

As scientists continue to sift through countless molecular events occurring in our cells, they will keep finding clues as to how our bodies and minds came to be.

“This is the tip of an iceberg in terms of the full repertoire of AS changes that likely have contributed major roles in driving evolutionary differences,” says Blencowe.

picpath

sites/default/files/2015-08-21-chickens.jpg

Evolution

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

Increases in rats, bedbugs and mosquitoes are unintended consequence of urbanization: U of T expert

Interested in publicly funded research in Canada? Learn more at UofT’s #supportthereport advocacy campaign

Read the study in the journal Science

Human ancestors originated in Europe – not Africa? U of T part of international team studying pre-human remains

Read more at the Washington Post

Read about the discovery in the Globe and Mail

Read more at Reuters

Giant sperm give male worms a reproductive edge, U of T research reveals

Why we're smarter than chickens