Ecology and Evolutionary Biology

This summer, where there's smoke there's probably fire

Rachel Sauer — Wed, 23 Apr 2025 21:01:58 +0000

This summer, where there's smoke there's probably fire Rachel Sauer Wed, 04/23/2025 - 15:01

Laura Dee

Controlled burns reduce wildfire risk, but they require trained staff and funding—this could be a rough year

Red skies in August, longer fire seasons and checking air quality before taking my toddler to the park. This has become the new norm in the western United States as wildfires become more frequent, larger and more catastrophic.

As an ecologist at the 51�Թ��, I know that fires are part of the natural processes that forests need to stay healthy. But the combined effects of a warmer and drier climate, more people living in fire-prone areas and vegetation and debris built up over years of fire suppression are leading to more severe fires that spread faster. And that’s putting humans, ecosystems and economies at risk.

To help prevent catastrophic fires, the U.S. Forest Service issued a 10-year strategy in 2022 that includes scaling up the use of controlled burns and other techniques to remove excess plant growth and dry, dead materials that fuel wildfires.

51�Թ�� researcher Laura Dee is an associate professor of ecology and evolutionary biology.

However, the Forest Service’s wildfire management activities have been thrown into turmoil in 2025 with funding cuts and disruptions and uncertainty from the federal government.

The planet just saw its hottest year on record. If spring and summer 2025 are also dry and hot, conditions could be prime for severe fires again.

More severe fires harm forest recovery and people

Today’s severe wildfires have been pushing societies, emergency response systems and forests beyond what they have evolved to handle.

Extreme fires have burned into cities, including destroying thousands of homes in the Los Angeles area in 2025 and near 51�Թ��, Colorado, in 2021. They threaten downstream public drinking water by increasing sediments and contaminants in water supplies, as well as infrastructure, air quality and rural economies. They also increase the risk of flooding and mudslides from soil erosion. And they undermine efforts to mitigate climate change by releasing carbon stored in these ecosystems.

In some cases, fires burned so hot and deep into the soil that the forests are not growing back.

While many species are adapted to survive low-level fires, severe blazes can damage the seeds and cones needed for forests to regrow. My team has seen this trend outside of Fort Collins, Colorado, where four years after the Cameron Peak fire, forests have still not come back the way ecologists would expect them to under past, less severe fires. Returning to a strategy of fire suppression − or trying to “go toe-to-toe with every fire” − will make these cases more common.

Proactive wildfire management can help reduce the risk to forests and property.

Measures such as prescribed burns have proven to be effective for maintaining healthy forests and reducing the severity of subsequent wildfires. A recent review found that selective thinning followed by prescribed fire reduced subsequent fire severity by 72% on average, and prescribed fire on its own reduced severity by 62%.

But managing forests well requires knowing how forests are changing, where trees are dying and where undergrowth has built up and increased fire hazards. And, for federal lands, these are some of the jobs that are being targeted by the Trump administration.

Parts of Cameron Peak in north-central Colorado that burned in a severe fire in 2020 showed scant evidence of recovery four years later, when this photo was taken. (Photo: Bella Olesky/51�Թ��)

Some of the Forest Service staff who were fired or put in limbo by the Trump administration are those who do research or collect and communicate critical data about forests and fire risk. Other fired staff provided support so crews could clear flammable debris and carry out fuel treatments such as prescribed burns, thinning forests and building fire breaks.

Losing people in these roles is like firing all primary care doctors and leaving only EMTs. Both are clearly needed. As many people know from emergency room bills, preventing emergencies is less costly than dealing with the damage later.

Logging is not a long-term fire solution

The Trump administration cited “wildfire risk reduction” when it issued an emergency order to increase logging in national forests by 25%.

But private − unregulated − forest management looks a lot different than managing forests to prevent destructive fires.

Logging, depending on the practice, can involve clear-cutting trees and other techniques that compromise soils. Exposing a forest’s soils and dead vegetation to more sunlight also dries them out, which can increase fire risk in the near term.

In general, logging that focuses on extracting the highest-value trees leaves thinner trees that are more vulnerable to fires. A study in the Pacific Northwest found that replanting logged land with the same age and size of trees can lead to more severe fires in the future.

Research and data are essential

For many people in the western U.S., these risks hit close to home.

I’ve seen neighborhoods burn and friends and family displaced, and I have contended with regular air quality warnings and red flag days signaling a high fire risk. I’ve also seen beloved landscapes, such as those on Cameron Peak, transform when conifers that once made up the forest have not regrown.

My scientific research group and collaborations with other scientists have been helping to identify cost-effective solutions. That includes which fuel-treatment methods are most effective, which types of forests and conditions they work best in and how often they are needed. We’re also planning research projects to better understand which forests are at greatest risk of not recovering after fires.

This sort of research is what robust, cost-effective land management is based on.

When careful, evidence-based forest management is replaced with a heavy emphasis on suppressing every fire or clear-cutting forests, I worry that human lives, property and economies, as well as the natural legacy of public lands left to every American, are at risk.

Laura Dee is an associate professor in the Department of Ecology and Evolutionary Biology.

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Controlled burns reduce wildfire risk, but they require trained staff and funding—this could be a rough year.

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Top image: U.S. Fish and Wildlife Service

College of Arts and Sciences faculty win 2025 Best Should Teach Awards

Rachel Sauer — Tue, 22 Apr 2025 13:30:00 +0000

College of Arts and Sciences faculty win 2025 Best Should Teach Awards Rachel Sauer Tue, 04/22/2025 - 07:30

Peter Hunt, Warren Sconiers and Josh Strayhorn will be honored during an awards ceremony May 1

Three College of Arts and Sciences faculty members have been recognized as 2025 Best Should Teach Award winners.

Peter Hunt, a professor of classics; Warren Sconiers, an associate teaching professor of ecology and evolutionary biology; and Josh Strayhorn, an associate professor of political science, will be recognized for their excellence in teaching and academic leadership at an awards ceremony from 6 to 9 p.m. May 1 in the CASE Chancellors Hall and Auditorium.

Peter Hunt (left), Warren Sconiers (center) and Josh Strayhorn (right) have been recognized as 2025 Best Should Teach Award winners.

The Best Should Teach Initiative was established in 1996 by Lindley and Marguerite Stiles to support the idea that “the best should teach.” It celebrates excellence in teaching at primary, secondary and higher education levels and supports the preparation of college and university faculty, as well as public school teachers, in their disciplinary fields.

Hunt, who has been a faculty member at the 51�Թ�� since 2000, is a classical Greek historian who studies warfare and society, slavery, historiography and oratory.

Sconiers trained as an insect ecologist, studying the effects of drought stress and changes in nutritional plant physiology and insect species composition. He also researches how to increase student engagement and learning in large classroom settings, focusing on peer-to-peer collaboration, self-efficacy, bridging biology teaching and research experiences and building instructor approachability.

Strayhorn, who joined the 51�Թ�� faculty in 2013, specializes in formal theory, political institutions and judicial politics. His research applies game-theoretic models in a variety of contexts. His work examines the implications of delegation, oversight and accountability mechanisms for outcomes within political and judicial hierarchies and for democratic governance.

The Best Should Teach Award ceremony is free and open to the public. The keynote speaker will be Alphonse Keasley, former associate vice chancellor in the Office of Diversity, Equity and Community Engagement at 51�Թ�� who has more than 30 years of experience as a faculty member, staff and administrator.

Best Should Teach events and awards are co-funded by the Ira and Ineva Baldwin Fund in the CU Foundation and Brian Good's private Best Should Teach Fund, with additional support from the Center for Teaching and Learning, the School of Education and the College of Arts and Sciences.

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Peter Hunt, Warren Sconiers and Josh Strayhorn will be honored during an awards ceremony May 1.

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Don’t fear the fungi

Rachel Sauer — Thu, 17 Apr 2025 13:30:00 +0000

Don’t fear the fungi Rachel Sauer Thu, 04/17/2025 - 07:30

Bradley Worrell

51�Թ�� mycologist Alisha Quandt says there’s little reason to fear a fungi-zombie apocalypse like the one imagined in the HBO hit TV series ‘The Last of Us’

Alisha Quandt prepared herself in advance to be asked by students and others about Sunday’s season 2 premier of “The Last of Us”—the hit HBO series that imagines a post-apocalyptic future where a fungal infection on a massive scale turns the majority of humanity into zombie-like creatures seeking to infect the last pockets of civilization.

It’s not that Quandt is a super-fan of the TV show (“I’m not into zombies, honestly,” she confesses), but as a mycologist—a scientist who studies fungi—she is used to getting asked about the TV show, specifically whether the grim future it imagines is anything people need to be worried about, or whether it’s simply harmless entertainment.

“I’m happy if it gets people excited about fungi. They’re so incredible,” says Alisha Quandt, a 51�Թ�� assistant professor of ecology and evolutionary biology.

“Especially when the TV show first debuted, it was definitely a topic people wanted to discuss,” says Quandt, a 51�Թ�� Department of Ecology and Evolutionary Biology assistant professor.

“And it seems like the topic (of infectious fungi) comes up in popular culture every five to 10 years. When I was starting my PhD, people were fascinated by the ‘Planet Earth’ TV series by David Attenborough, where this ant infected by Ophiocordyceps unilateralis staggers around, being controlled by the fungus. Then later, the Last of Us videogame came out, which really got people excited about (zombie) fungi.”

Quandt did her PhD research studying Cordyceps-like fungi, which is the type of pestilence the TV show identifies as the culprit for turning civilization into a hellscape populated by zombies controlled by the spiky fungi tendrils sprouting from their heads. For the record, Quandt finds that scenario very unlikely, for a variety of reasons.

No need to panic

For starters, the TV show imagines a worldwide outbreak is caused by Cordyceps-contaminated food. However, Quandt says most fungal infections in humans are caused by inhaling spores or through contact with the eyes or skin—and not through the digestive tract. She notes that in many parts of the world, people have been ingesting Cordyceps fungi for decades without incident, because they believe they contain beneficial properties.

“I’ve eaten Cordyceps in Asia, in Korea and China,” says Quandt, who remains unzombified. “It’s considered a part of traditional Chinese medicine, especially certain species. Even here in the U.S., you can find Cordyceps in coffees and teas, for example. They sell them at stores in 51�Թ��.”

Quandt says another reason not to be overly concerned about Cordyceps is that many of them are “specialists” that have a very narrow range of hosts that they infect, down to a specific family of ant or spider. While some Cordyceps can transition from infecting one type of arthropod to another, or to jump from infecting an insect to another fungus, she says making the leap to a healthy human being is remote.

What’s more, the average human body temperature of 97 to 99 degrees Fahrenheit is not an environment that’s hospitable for many fungi, although Quandt acknowledges there are exceptions. “The Last of Us” imagines a future in which global warming has raised Earth temperatures to a point where mutated Cordyceps zombie fungi could live comfortably in human hosts, but Quandt notes that ambient temperatures of even 90 degrees Fahrenheit are still cooler than the human body.

“That’s a hard path for me to follow,” she says of an environmental change that would allow Cordyceps to evolve in such a way. “There’s a lot of assumptions that would go into that trajectory.”

51�Թ�� scientist Alisha Quandt finds the scenario from "The Last of Us" in which a Cordyceps-like fungi causes worldwide zombification very unlikely, for a variety of reasons. (Photo: HBO)

Beyond those arguments, Quandt says there is an even more important one as to why humans don’t need to start doom prepping for a fungi apocalypse.

“My argument about why we shouldn’t be worried about a fungal pandemic is that our bodies, when fully immunocompetent—meaning healthy human bodies—are extremely well equipped to deal with fungal propagules (spores) that come into contact with our bodies, mostly through our lungs,” she says. “Fungi have this cell wall that is made up of stuff that our bodies do not make. So, our bodies are really good identifying and dealing with that.”

Quant says fungal infections do pose a risk to people whose immune systems are compromised—particularly if they have taken a heavy dose of antibiotics, because those can kill off good bacteria, which can lower resistance to harmful fungi.

“Once our immune system goes away, which could handle those types of (fungi), we have so few antifungal drugs to treat fungal infections compared to the myriad of antibiotics that we have to treat bacterial diseases,” she says.

For the immunocompromised, Quandt says one of the most concerning fungi—which just cropped up in recent years and has spread worldwide—is Candida auris.

“It is a really concerning human pathogen because it is what we call nosocomial, meaning it is hospital related. People get these infections in hospitals, and once it’s in a hospital, it can be almost impossible to get rid of it,” she says.

“People will use all kinds of bleach and ethanol but it’s very hard to get rid of the yeast once it gets into a hospital room. And the fully immunocompetent, like nurses and doctors who are not sick, can end up spreading it from room to room to sick, often elderly, patients. Unfortunately, there’s not a good defense on the ground, so to speak, once Candida auris takes hold.”

But while “opportunistic pathogens” like Candida auris can pose a risk to the immunocompromised, the number of fungal diseases that could be described as “primary pathogens”—meaning they can infect and potentially cause serious health issues for healthy individuals—is less than a handful, Quandt says.

One primary pathogen that can be found in the United State is Valley Fever, which is primarily located in New Mexico, Arizona and southern California. Farming, construction or other practices that disrupt the soil can release the fungi’s spores, which people can then breathe into their lungs. Once inhaled, Valley Fever can potentially cause fever, cough, tiredness, shortness of breath and, in limited cases, serious conditions such as pneumonia and meningitis.

“But those are the rarer things, and I’m still not worried about them becoming common because they’re still not being spread from person to person,” she says.

In contrast with the way “The Last of Us” portrays fungi as an existential threat, Quandt sees a type of virus that’s already well-known to the scientific community and the public alike as a much greater risk for causing a global pandemic. The World Health Organization estimates the COVID-19 pandemic killed 14.9 million people worldwide between January 2020 and December 2021.

“As we’ve recently seen, unfortunately, there are a lot of other places to look for more likely suspects for (global pandemics). Things that were predicted by a lot of great investigative journalists and epidemiologists, like coronavirus and other zoonotic diseases (which jump from animals to humans), pose a much greater threat to mankind,” she says.

“As we’ve recently seen, unfortunately, there are a lot of other places to look for more likely suspects for (global pandemics). Things that were predicted by a lot of great investigative journalists and epidemiologists, like coronavirus and other zoonotic diseases (which jump from animals to humans), pose a much greater threat to mankind.”

And now, back to the show

Even beyond the fact she’s not into zombies, Quandt says her training as a mycologist can get in the way of her enjoyment of “The Last of Us” as entertainment, based upon the few episodes she has watched.

“I’m probably a little too close to watch the show—especially the fruiting bodies,” she says. “Sometimes they would show a person who is dead up against a wall, and the fruiting structures look life shelf fungi,” she says.

“Those are related to mushrooms—they’re not related to (fungi) that are molds, like Cordyceps. The artistry was beautiful, so they did a good job visually, but it’s just completely inaccurate. So, it does take you out of it a little bit to watch as an expert; you have to really suspend belief.”

Another scene that inspired disbelief for Quandt was a flashback episode—prior to the fungal pandemic—when a mycologist in Jakarta is asked by representatives of the country’s military to provide guidance on how to proceed after a group of workers in a building are found to be infected with early cases of the Cordyceps contagion. After surveying the infected, the mycologist gives the military members a chilling one-word answer: “Bomb!” (As in, bomb the entire country to try to prevent the infection from spreading.)

“My husband was watching the show with me. He paused it there and he’s like, ‘What should they do?’ I was like, ‘Get all the antifungals that you can. Get all the major ones and then get the rare ones—and start pumping these people with IVs, or all the people that you think might be exposed and get going on it.’ But the fact she said ‘bomb!’ I almost found it funny, but I was also like, ‘Oh, my God, that’s so dramatic.’ Still, it’s a TV show, and I acknowledge that.”

While Quandt may opt not to watch more episodes of “The Last of Us,” she says if the TV show raises public awareness about fungi—even if the details in the show are not entirely correct—she is all for it.

“I’m happy if it gets people excited about fungi,” she says. “They’re so incredible.”

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51�Թ�� mycologist Alisha Quandt says there’s little reason to fear a fungi-zombie apocalypse like the one imagined in the HBO hit TV series ‘The Last of Us.'

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Top image: HBO

No, it’s not Darwinism if you get hurt while doing something dumb

Rachel Sauer — Mon, 10 Feb 2025 18:13:30 +0000

No, it’s not Darwinism if you get hurt while doing something dumb Rachel Sauer Mon, 02/10/2025 - 11:13

Bradley Worrell

In honor of Darwin Day Feb. 12, 51�Թ�� evolutionary biologist Daniel Medeiros explains what we get right and wrong about Darwinism

For evolutionary biologists, the big day is imminent.

No, not Valentine’s Day.

For many scientists, educators, historians and humanists, the upcoming event of note is Darwin Day, which supporters say is a time to reflect and act on the principles of intellectual bravery, perpetual curiosity, scientific thinking and a hunger for truth, as embodied by Charles Darwin.

Daniel Medeiros, a 51�Թ�� professor of ecology and evolutionary biology, notes that while Charles Darwin didn't originate the idea of evolution, "I think he did the best, most comprehensive way of presenting things."

The noted British naturalist and biologist is widely recognized for his book On the Origin of Species, which is considered the foundation of modern evolutionary biology. Darwin Day is celebrated internationally every Feb. 12, the anniversary of Darwin’s birth on Feb. 12, 1809, outside of London.

Scientists say it’s hard to quantify the impact Darwin had on evolutionary theory. At the same time, a lot of misconceptions have arisen regarding his theories, and some propagandists have used his scientific theories to support a variety of ideas he never endorsed and, in some cases, would likely be appalled by.

Recently, Professor Daniel Medeiros with the 51�Թ�� Department of Ecology and Evolutionary Biology talked with Colorado Arts and Sciences Magazine about some of the mistaken ideas associated with Darwin while also delineating why some of his scientific concepts can be so difficult to grasp. His responses have been lightly edited for style and condensed for space.

Question: One idea about Darwin is that he originated the idea of evolution. True or false?

Medeiros: False. I actually had a colleague, Ned Friedman, a plant evolutionary biologist, who taught a whole course on evolutionary thinking before Darwin. And in fact, Darwin’s own grandfather, Erasmus Darwin, had some pretty clear evolutionary thoughts and logic. I think Darwin collected the most data and articulated the best case for evolution by natural selection, but he didn’t come up with it out of whole cloth.

That’s how things happen in evolution—there’s ‘convergence.’ Similar solutions can occur in different lineages around the same time or given the same environmental pressures. That’s the idea of evolution by natural selection; I think several scientists came to that conclusion simultaneously. So, it wasn’t all Darwin, but I think he did the best, most comprehensive way of presenting things.

Question: What about the idea that Darwin’s theory on evolution encompasses the origins of life?

Medeiros: I think he may have hypothesized on the origin of the living creature from a primordial soup of chemicals, but I don’t think he knew enough about chemistry or cell biology to go beyond that. I don’t know how he would have even begun to hypothesize about cellular evolution.

Question: What about the idea that Darwin believed humans are descended from apes?

Medeiros: That’s kind of a tough one, even for some of my students in my upper division class. The proper way to think about evolution is as a family tree. The idea that humans evolved from a chimp or humans evolved from a monkey; specifically, what you think of a modern monkey, is incorrect. It’s easy to conceive given that those modern species are clearly related to us, but we are not descended from them.

Now, our last common ancestor looked something like a chimp and would definitely be classified as a “great ape”. We also had an ancestor who looked something like a monkey, but technically, ‘we came from a monkey’ is not how you would describe it in evolutionary biology terms. We evolved from species that were chimp-like, but we’re not chimps and we did not come from modern monkeys.

During his visit to the Galapagos Islands, Charles Darwin observed that different finch species had varying beak lengths, which supported his theory that species evolve to exploit their food sources and habitats. (Illustration: from Journal of Researches by Charles Darwin)

Any species that’s alive today is a successful modern species, as much as we are. If it’s around today, it’s a survivor. It’s a successful species that has its own set of innovations. If it’s living today, it’s its own success story.

Question: What about the idea some attribute to Darwinism that modern humans aren’t evolving?

Medeiros: That’s incorrect. That’s a property of all living things—that they are always changing. It’s not something you can stop. DNA is always accumulating mutations. There’s always genetic variation, and that variation responds to the environment. In the short window of time we have been around, it’s hard to see, but it’s true.

I’m not sure how we’re evolving, but there’s no organism that’s not evolving. So, we’re changing for sure, in some way, but I don’t know how. It will be interesting to see.

Question: There’s also this idea associated with Darwinism that animals are deliberately attempting to adapt to their environments. Accurate or not?

Medeiros: That’s a misconception. The word ‘evolution’ means unfolding, originally, which implies that you have some truth or something that’s unfolded or revealed. But it’s actually much more chaotic and there’s a huge random factor.

From the organism’s perspective, they’re just throwing out babies with variations. And hopefully, one of them sticks. And if one sticks, your lineage hangs around and has another chance for more mutation. So, it’s random and it’s chaotic.

Andthere are limitations. Species go extinct all the time. Maybe their environment changed too quickly, and they were unable to adapt. Maybe they just didn’t hit upon the right mutations, or there could be constraints to their development or their genome that wouldn’t allow adaptive traits to evolve and they go extinct. That’s common.

(The word) ‘evolved,’ in terms of how people use it in common language, it’s like, ‘Oh, I evolved. I became better.’ It’s about this idea of better and more. But then extinction is evolution, too. It’s just change over time, however, that manifests itself.

A cool thing that I teach in my class is that a lot of animal evolution since the Cambrian or a little later—has been about loss; trimming down, getting rid of what you don’t need. I think that’s one thing that’s not really recognized too much, that evolution is not always—or even mostly—about gaining fancy new features. It’s not necessarily this march toward more and more sophistication. It’s a lot about use it or lose it—about losing features that are not adaptive anymore. A lot of evolutionary change, especially in animals, is loss.

Then you have these blockbuster new things, like feathers, which are a huge innovation, or a turtle shell, or the human brain, which is another huge innovation. But then, even more than that, what makes a lot of species different from each other is that they’ve lost different things.

Charles Darwin, seen here in an 1881 portrait, published his theory of evolution in his 1859 treatise On the Origin of Species. (Photo: Hulton Archive/Getty Images)

Question: Why do you think it seems so hard for people to grasp the idea of evolution?

Medeiros: Evolution is hard to understand because it’s inherently about processes beyond any individual’s experience. It’s about things happening on a scale of tens, hundreds, thousands and millions of years. That’s hard for us to fathom, and it’s not necessarily intuitive.

It’s kind of like the idea of the earth spinning around the sun. That’s not intuitive. If you look outside, that’s not what you see happening. You don’t feel like you’re spinning. The sun moves up over you. It defies your experience as a human.

So, it’s easy to have misconceptions and I don’t fault people for that. It’s a hard, hard concept just by itself, much less the implications where it could be perceived as taking human beings down several notches, as just another animal that evolved.

Question: There is an idea in some quarters that evolution and religion, whether it's Christianity or another faith, are incompatible. Any thoughts on the notion that if you believe in one of those ideas you can’t believe in the other?

Medeiros: I think that’s mostly on the religion side of things. It’s really up to you, whether you, as a religious person, can believe in evolution. That’s a great thing about religion: If you want to incorporate evolution into it, you could surely work it in, but if it somehow interferes with your beliefs, you won’t. You can shape your religion to exclude any kind of science, if you want.

In my education, I’ve had several biology teachers, evolutionary biologists and otherwise, who were quite religious people and (evolution) didn’t interfere with their belief.

As I understand it, Darwin himself was a religious person for most of his life, and finally ended up calling himself agnostic. You can see some of that in his writing. With some (discoveries) it was like, ‘OK, where does this place God? This evidence maybe puts the role of God in a different place than I was taught when I was younger.’ I think he used some language like that in his writing.

I’m not a historian, but I don’t think Darwin ever excluded a role for religion.

Question: It seems like not long after Darwin published The Origin of Species, people began using his work to promote their own political, religious or ideological agendas?

Medeiros: Yes, 100%. I couldn’t give you the exact timing on when that started to happen, but I think it was while he was still alive that people began to formulate ideas around his work. I think that’s not uncommon: You figure out some scientific truth and there will be people to exploit it for good and bad.

Evolution by natural selection and survival of the fittest—all of those touch phrases and concepts—in isolation have been used to justify some very horrible things.

Question: The Darwin Awards were created a few years back as a tongue-in-cheek honor bestowed on people who removed themselves from the gene pool by doing something really dumb. How far removed are those awards from anything associated with the actual British biologist?

Medeiros: I remember first hearing about them in graduate school. At the time, I thought it was humorous, but after I became a parent, the idea of people getting hurt and dying in weird ways was no longer so funny.

And really, that’s not how natural selection works. It’s not like, you’re an evolutionary loser, so you get attacked by a lion because you’re dim-witted.

Really, it’s all about the numbers at the margins. For example, with this particular adaptive allele, you have lineage that has 5% more offspring—and you do that over many generations and throw in some random environmental change—and they’re the fittest. But their fitness is just kind of at the margins and there’s a lot of luck involved, too.

So, it’s not as clear as, ‘Oh, this is person’s a ding-dong; they strapped themselves to a rocket' or whatever. That’s not an accurate representation of Darwin’s ideas.

Question: Will you be doing anything for Darwin Day this year?

Medeiros: In past years I’ve given a talk about Darwin, mentioning some things about the ‘modern synthesis’ concept, which includes things that Darwin was not aware of at the time—filling in some of the gaps he was unaware of—like DNA and genes.

That’s not to take anything away from Darwin. It’s fun to read Darwin because he’s so modern in how he thought and deduced things. I think a lot of biologists feel like, ‘Well, if I was back then, that’s how I would have figured things out, too.’

But to answer your question, nothing special planned, like reading from Origins. I might celebrate by going to my lab and writing a grant. Also, my youngest son has the same birthday as Darwin, so we will be focusing on that! I think Darwin would appreciate that … by all accounts he wasn’t just a great scientist, but a really devoted dad.

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In honor of Darwin Day Feb. 12, 51�Թ�� evolutionary biologist Daniel Medeiros explains what we get right and wrong about Darwinism.

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Top illustration: Khawar Sohail Siddiqui/ArtStation

Katharine Suding named a 2025 Franklin Institute Bower Award winner

Rachel Sauer — Mon, 10 Feb 2025 16:17:16 +0000

Katharine Suding named a 2025 Franklin Institute Bower Award winner Rachel Sauer Mon, 02/10/2025 - 09:17

51�Թ�� distinguished professor recognized for ‘transformative contributions to restoration ecology’

Katharine Suding, a 51�Թ�� distinguished professor of ecology and evolutionary biology, has won The Franklin Institute’s 2025 Bower Award and Prize for Achievement in Science and been named a Franklin Institute Laureate.

Suding is recognized for making “transformative contributions to restoration ecology by increasing our understanding of degraded ecosystems and their recovery dynamics. Her work addresses urgent environmental and societal challenges, and guides policies and practices of ecological restoration, biodiversity conservation and sustainable ecosystem management,” notes The Franklin Institute.

The Bower Awards honor extraordinary excellence in science, technology and business. Suding and her eight colleagues in the 2025 Franklin Institute Laureate cohort are cited as “true visionaries, pushing the boundaries of innovation to find solutions to some of the world’s most pressing challenges—and their achievements are transformative.”

"I could not have done this work if not for amazing collaborations with students, postdocs and colleagues, as well as indispensable partnerships with restoration practitioners," says 51�Թ�� researcher Katharine Suding (second from left, blue baseball cap). (Photo: Katharine Suding)

“I am incredibly honored to receive The Franklin Institute’s Bower Award for Achievement in Science,” Suding said. “Ecosystem restoration is tasked with solving complex environmental challenges facing the world today, a discipline that well represents Benjamin Franklin’s spirit of innovation and application. I could not have done this work if not for amazing collaborations with students, postdocs and colleagues, as well as indispensable partnerships with restoration practitioners. This award is for them, for the field and for everyone working to bring back nature.”

Suding is a plant community ecologist who works at the nexus of ecosystem, landscape and population biology. Her research aims to apply cutting-edge “usable” science to the challenges of restoration, species invasion and environmental change. She and her research group work with a range of conservation groups, government agencies and land managers to provide evidence-based solutions that take into account biodiversity, human well-being and management opportunities.

They employ a combination of long-term monitoring, modeling and experimental approaches in settings that range from alpine tundra to oak woodlands to grasslands. Common themes of their work include plant-soil feedbacks, functional traits, species effects on ecosystem processes and non-linear and threshold dynamics.

Founded in 1824, The Franklin Institute of Philadelphia strives to honor the legacy of Benjamin Franklin by presenting awards for outstanding achievements in science, engineering and industry. As the oldest comprehensive science and technology awards program in the United States, The Franklin Institute Awards Program has recognized more than 2,000 of the most pioneering scientists, engineers, inventors and innovators from around the world.

Previous laureates include Nikola Tesla, Thomas Edison, Pierre and Marie Curie, Max Planck, Orville Wright, Albert Einstein, Edwin Hubble, Frank Lloyd Wright, Ruth Patrick, Jacques Cousteau, Stephen Hawking, Martin Rees, Gordon Moore, Shuji Nakamura, Jane Goodall, Elizabeth Blackburn, Bill Gates, Jim West and Gerhard Sessler, Cornelia Bargmann, John Goodenough, Jim Allison and Frances Arnold.

Suding and the other members of her laureate cohort will be honored in Philadelphia the week of April 28–May 2. Awards will be bestowed during a ceremony at The Franklin Institute on May 1 hosted by Chief Astronomer Derrick Pitts.

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51�Թ�� distinguished professor recognized for ‘transformative contributions to restoration ecology.'

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Katharine Suding (second from right, blue jacket) and colleagues work in a greenhouse. (Photo: Matt Tallarico)

Sand verbena uses grains of sand to deter herbivores

Rachel Sauer — Thu, 19 Dec 2024 19:41:09 +0000

Sand verbena uses grains of sand to deter herbivores Rachel Sauer Thu, 12/19/2024 - 12:41

Jeff Mitton

Apparently, herbivores are not fond of chewing sandpaper

Sand verbena, Abronia fragrans, has a moth pollination syndrome, or a suite of floral characters modified by natural selection driven by moth pollination. Its flowers are open all night but closed all day, and long corolla tubes prevent bees from taking nectar but are ideal for moths with long tongues.

Moths follow plumes of floral fragrance from sand verbena until they are within sight of the bright, conspicuous white globes of 25 to 80 flowers, where they sip a nectar reward.

Although sand verbena has a large geographic range, it is limited to sandy habitats in Texas, New Mexico, Arizona, Utah, Colorado, Oklahoma, Kansas, Wyoming, Montana, Nebraska, South Dakota and North Dakota. While sand verbena is described as having white flowers that open only at night, populations in northern Texas and southwestern Oklahoma have a range of flower colors from light pink through fuchsia, and they also differ from most populations in the times that flowers open and close.

The plants with pink or fuchsia flowers remain open until late morning, and they reopen in early evening, allowing considerable visitation by bees and butterflies. Measurements of pollination success in the pink and fuchsia populations showed that diurnal or daytime pollination contributed 18% of the pollination success, in contrast to nothing at all in the remainder of the geographic range of the species.

Dwarf lupine with patches and particles of sand on its flowers, leaves and stem. (Photo: Jeff Mitton)

These data are consistent with the hypothesis that diurnal pollinators were a selective force producing and maintaining novel flower color and diurnal presentation of open flowers in the mornings and late afternoons. The long corolla tubes frustrate bee efforts to collect pollen or nectar but hold nectar available to virtually all butterflies.

Butterflies are visiting diurnally—the most common among them is the skipper Lerodea eufala, the Eufala skipper. These data and other observations suggest the hypothesis that the Eufala skipper applied selective pressure to change flower color from white to pink or fuchsia and to modify the times that flowers open and close.

How could a butterfly apply selection pressure? This terminology unintentionally suggests that the butterflies had a plan and the organization to apply it. But that was not the case. If some flowers did not close exactly at sunrise and if a small butterfly pollinated them, enhancing their seed set, the genes that influenced tardy closing of flowers would become more common in the next generation.

The butterfly did nothing more than sip nectar from a large globe of flowers, nor did the sand verbena do anything to achieve an intended goal. The metric of natural selection is the relative number of offspring produced by competing genotypes of sand verbena. Genes that had been rare produce more seeds, making those genes more common.

Sand verbena is in the genus Abronia, which has about 20 species, all in North and Central America. All thrive in sandy environments, and it is known that 14 of the 20 species have psammophory, a defense to herbivory that is more commonly called sand armor. The armor is assembled when wind-blown sandy grit adheres to sticky exudates on stems and leaves.

I first encountered psammophory when photographing dwarf lupine in the Maze in Canyonlands National Park, and since then I thought it was a rare defense. But a scientific article whose title begins with "Chewing sandpaper" lists more than 200 psammophorous species in 88 genera in 34 families.

Sand armor is not a rare defense; it is geographically widespread and has evolved many times. Experimental studies show that sand armor reduces herbivory—remove it from stems and leaves, and the plant suffers more herbivory than when the armor was intact. Add more sand, and the plant suffers less herbivory.

While sand verbena has a large geographic range, some species of Abronia have tiny geographic distributions. One example is Yellowstone sand verbena, A. ammophila, which is adapted to and endemic (found nowhere else) to the lake shores in Yellowstone National Park.

An obligate relationship was found recently when a new species of moth, Copablepharon fuscum, was discovered in 1995 on the shores of the Salish Sea between Georgia Straight and Puget Sound. The sand-verbena moth was found on just a few beaches and spits on Vancouver Island and Whidbey Island, and it only occupies sites with windblown sand and large and dense populations of A. latifolia, yellow sand verbena, which is found along Pacific Shores from Baja to British Columbia.

The sand-verbena moth uses yellow sand verbena as its host plant, meaning that it is the site of oviposition and the sole food consumed by the caterpillars. The caterpillars have specialized mouth parts allowing them to manipulate around grains of sand.

I know I will never see a sand verbena nor a dwarf lupine without the phrase "chewing sandpaper" popping into my thoughts.

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Top image: Sand verbena usually presents white blooms but response to a pollinator can turn a population pink or fuchsia. (Photo: Jeff Mitton)

Cetacean science: A new understanding of humpback whale genetics

Rachel Sauer — Mon, 02 Dec 2024 16:44:47 +0000

Cetacean science: A new understanding of humpback whale genetics Rachel Sauer Mon, 12/02/2024 - 09:44

Blake Puscher

How a team of 51�Թ�� PhD students produced the first chromosome-level reference genome for humpback whales

Humpback whales are striking animals, not only because of their size, but also because of their complex vocalizations, acrobatic swimming and thousand-mile migrations.

Moreover, they hold a vital role in marine ecosystems, as their fecal matter, which is released as floating plumes, fertilizes the upper layer of the ocean and stimulates the growth of the photosynthesizing plankton there. These plankton are the basis of the marine food chain and are major contributors to the global carbon cycle.

PhD student Maria-Vittoria Carminati worked with colleagues to create the first chromosome-level reference genome for humpback whales.

Despite the importance and charisma of humpback whales, research into the species has been limited by the lack of complete genetic information.

Maria-Vittoria Carminati, a PhD student in the 51�Թ�� Department of Ecology and Evolutionary Biology, changed this when, along with Associate Professor of Ecology and Evolutionary Biology Nolan Kane and a team of fellow graduate students*, she created the first chromosome-level reference genome for the species.

Moving the needle

Carminati became an attorney in 2008 and worked in that field until recently. “I came to the realization that I wanted to do something more meaningful with my brain power,” she says. “That’s why I switched to science: I thought it would allow me to make greater contributions to society.

“So, three years ago, I went back to college and got my bachelor’s in ecology and evolutionary biology.” After that, she started her PhD at 51�Թ��. There remained the question of what she would do to “move the needle forward,” but Carminati knew it would probably involve the ocean.

“I’m a diver, I’m a dive instructor, I like to sail even though I’m not very good at it,” she continues. After seeing a humpback whale in person one day, she started reading about them and found a paper that mentioned they were splitting into different subspecies. “I thought the paper was trying its best, but I don’t think it had the tools it needed to be assertive about what it was saying.”

One of those tools is a reference genome. So, Carminati went to experiment.com for funding and to Cantata Bio for the sequencing. She got a permit to sequence the humpback DNA sample from the National Oceanic and Atmospheric Administration and obtained the sample itself from the National Institute of Standards and Technology.

The sample was from the kidney of an orphaned whale calf that was beached and died on the shore of Hawaii Kai.

Cantata Bio’s sequencing yielded half a terabyte of data, which Kane tasked a class to help Carminati process.

A humpback whale swimming off the coast of Moorea, French Polynesia. (Photo: Charles J. Sharp/Wikimedia Commons)

The basics of genome sequencing

Genome sequencing is the process scientists use to determine a large amount, if not the entirety, of an organism’s DNA, which is packaged in threadlike structures called chromosomes. Because the entire length of a chromosome cannot be sequenced at once, several strips are sequenced and then combined in what is known as a genome assembly.

The product of the researchers’ work is called a reference assembly. According to Carminati, this means that the chromosomes are represented well enough to be used in comparison with the DNA of other organisms. “It’s like having the full book of an organism’s DNA,” she says. “In our case, we are only missing 0.0003% of the entire genome.”

This level of accuracy distinguishes their assembly from others, such as the scaffold-level assembly of the humpback whale genome that already existed. To continue the book analogy, this level of assembly can be compared to a collection of passages that cannot be definitively ordered or associated with a particular “chapter,” or chromosome.

Such uncertainty is partially the result of short read lengths. “Short reads are cheaper, so often, labs will do short reads,” Carminati says. “The problem with a short read is that you are only getting, say, a couple of sentences from each page in the book.” These few sentences are less distinctive than longer passages, which leaves more doubt in the final genome assembly.

The DNA in the researchers’ assembly was created from long reads, which allows it to be organized into chromosomes. Their assembly also had a high depth, which is to say that reads were performed 30 times to ensure accuracy, consistent with the platinum standard introduced by Philip Morin of the Cetacean Genomes Project.

Insight and annotation

While this chromosome-level genome was created too recently for researchers to have made discoveries by using it, Carminati says that the resource can be expected to provide insights into interesting traits of humpback whales, such as their cell regulation, large size and cancer resistance, as well as the formation of subspecies and other elements of genetic variation.

A humpback whale breaches off the coast of Tahiti. (Photo: Jérémie Silvestro/Wikimedia Commons)

“We are right at the beginning of this process,” Carminati explains, “but the reason that you can start making those insights is because if you have a platinum-level assembly, you have a far greater degree of certainty of what genes are and are not there.” This will allow scientists to tell with certainty whether a gene exists, does not exist or exists and is expressed multiple times.

“That goes to cell regulation and cancer resistance,” Carminati says, “because, for example, if you have a lot of genes that relate to cell regulation, cell repair and cell control, that indicates a cancer-preventing or cancer-halting mechanism because cancer is the result of the misregulation of cell division.

“So, if you have multiple genes like this, that might be one way that these enormous, 40-ton creatures are able to get so big and have so much cell division but not develop cancer.”

Other insights could be provided by synteny analyses, which are comparisons between sets of chromosomes. According to Carminati, these comparisons can help identify conserved areas: regions of genes that are unlikely to be rearranged between generations. When genes are together in a conserved area, this could indicate that they work together or are necessary for each other’s function.

The researchers performed a synteny analysis between the chromosomes from the humpback whale reference genome and the chromosomes of a blue whale. Synteny analyses can also indicate evolutionary relationships, and their analysis showed that there is a high level of consistency in the evolutionary relationships between the two species.

They also used BUSCOs (benchmarking universal single-copy orthologs), which are genetic reference guides developed in Switzerland, to evaluate genome completeness. BUSCO genes for mammals correspond to common mammalian traits, Carminati says, like lactation, placentas and live births. This analysis showed high completeness, too, but also represents another possible application of the reference genome: comparing whales to other mammals.

“We said, ‘What genes within this mammal BUSCO reference list do both of these creatures [humpback and blue whales] have, but more interestingly, which ones do they not have?’” Spending more time with this sort of analysis in the future could provide information about the evolution of whales, since missing mammalian genes would have either served no purpose to whales or even been counterproductive.

Finally, the researchers asked Cantata Bio start to annotate the reference genome. “Annotation tells you what genes are where,” Carminati says, and it is a necessary part of genome analysis. The annotation has not been made public yet, since the process is ongoing.

However, the research has already drawn attention, since Carminati presented it at the International Marine Conservation Conference in Cape Town, South Africa, last month. “So,” Carminati says, “I went from seeing a humpback whale in Hawaii to presenting a genome in Cape Town. Four years ago, I was trying cases. It is a very surreal trajectory.”

*Contributing graduate students are Vlonjat Lonnie Gashi, Ruiqi Li, Daniel Jacob Klee, Sara Rose Padula, Ajay Manish Patel, Andy Dick Yee Tan and Jacqueline Mattos.

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Humpback whale with calf off Moorea, French Polynesia (Photo: Charles J. Sharp)

Trailing fleabane looks delicate, but it flowered through a drought

Rachel Sauer — Tue, 26 Nov 2024 23:13:46 +0000

Trailing fleabane looks delicate, but it flowered through a drought Rachel Sauer Tue, 11/26/2024 - 16:13

Jeff Mitton

Flower was once thought to repel fleas, a belief long-since debunked

According to the U.S. Drought Monitor, 51�Թ�� County was in severe drought in September and the beginning of October this year. On Oct. 14, I went up on Flagstaff Mountain to see what was blooming and to check the condition of some small cacti, Missouri foxtails.

The foxtails were shriveled and seemed to be shrinking into the earth, a common plight for cacti in drought conditions. But my attention quickly shifted to some delicate daisies—these were the only flowers blooming in the prolonged drought.

The flowering species was flowering was Erigeron flagellaris. The plants were about 8 inches tall and had the typical daisy bloom with numerous slender, white petals radiating from a central yellow disc. Erigeron is a large genus in the family Asteraceae, commonly called composites, because each of the blooms is a composite of yellow disc florets in the center and white ray florets radiating.

Each "petal" is a ray floret, a flower that is solely female and fertile. Each of the disc florets is bisexual and fertile. An E. flagellaris bloom has 40 to 125 ray florets and even more disc florets.

In addition to seeds produced by both ray and disc florets, E. flagellaris reproduces asexually by producing stolons, stems that grow horizontally, touching ground at each node.

Erigeron flagellaris, or trailing fleabane, flowers and their mature seeds (Photo: Jeff Mitton)

Contact with the ground stimulates a node to grow a new cluster of roots that support the growth of upright stems, leaves and more flowers. This asexual reproduction creates a spreading clone that, under the best of conditions, resembles a mat. The proliferation of stolons suggests its common names, trailing fleabane and whiplash fleabane. Strawberry plants also spread with stolons, but gardeners usually call them runners.

The genus Erigeron has about 200 species, many of them in North America and all with the common name fleabane. The name, originally from Old English and first used in 1548, comes from the belief that the plant's smell would repel fleas from a dwelling. Plants were either burned or hung in sachets. Both belief and practice were dispelled long ago—fleabanes do not banish fleas.

The Navajo were resourceful at finding preparations of plants that had practical uses for dyes and medicines, and they found a way to use the astringent properties released from crushed leaves of trailing fleabane. They would chew the leaves and then place the moist pulp directly on wounds to stop the bleeding.

Description of the scent of trailing fleabane is elusive. The website Southwest Colorado Wildflowers lists citations in which the scent has been described as spicy, camphor-like, ill-scented, mysterious and downright weird. Chemical studies of fleabanes shows that their fragrances come from essential oils, volatile liquids containing chemical compounds synthesized by the plant.

I was not able to find a study of the essential oil of trailing fleabane, but several other fleabanes have been studied, and all reveal a bewildering diversity of biologically active compounds. For example, a study of the essential oil in E. floribundus, which has the common names tall fleabane and asthma weed, has 85 biologically active compounds. Concentrations of the various compounds differ among fleabane species that have been studied, resulting in a diversity of fragrances.

The constituents in essential oils are undoubtedly expensive to synthesize, but many studies have shown that they contribute to the defense of the plant against herbivores, microbes and fungi. I see a parallel between the essential oils of fleabanes and the resins of pines, firs and spruces.

In fact, limonene is a component of both essential oils and resins. Laboratory studies have shown effective defensive activity of limonene in the oil of E. floribundus, and populations studies have shown that mountain pine beetles eschew ponderosa pines with high levels of limonene.

In summer months, as people camp, hike and generally play in the mountains, one often hears comments about the pleasant fragrance of stands of ponderosa pine, or a spruce and fir forest. But I have never noticed the smell of fleabanes. It is a certainty that herbivores such deer and rabbits note the smell and shun the plants; it is the primary defense of daisies.

The essential oils extracted from several fleabane species can be purchased on the web, but I am sure that sniffing a concentrated concoction of biologically active chemicals from a bottle and nasally inhaling in a field of fleabanes would be different experiences. Let's remember to go fleabane sniffing next summer.

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Trailing fleabane is small and appears delicate, but it is hardy and well defended. (Photo: Jeff Mitton)

What we don’t know about fungi could hurt us

Rachel Sauer — Wed, 20 Nov 2024 23:03:17 +0000

What we don’t know about fungi could hurt us Rachel Sauer Wed, 11/20/2024 - 16:03

Blake Puscher

51�Թ�� researchers demonstrate how knowledge gaps hinder conservation efforts

Over the past century, conservationists have become more effective in sounding the alarm about species at risk of extinction. However, some groups, such as fungi, remain understudied, and the level of risk they face is unknown.

This isn’t because fungi are insignificant; according to the U.N. Decade on Restoration, fungi are important contributors to soil health and soil carbon sequestration, or the process of removing carbon dioxide from the atmosphere and storing it in soil. However, because so many fungi are poorly studied, the full extent of their contributions to global ecosystems remains unknown.

51�Թ�� scientist Alisha Quandt and her research colleagues argue for the importance of closing taxonomical knowledge gaps related to fungi.

The importance of closing these gaps in taxonomical knowledge, or knowledge from the field of science concerned with the classification of organisms, are explained in a study by C. Alisha Quandt and Danny Haelewaters of the 51�Թ�� Department of Ecology and Evolutionary Biology, as well as colleagues from several European institutions.

In the study, Laboulbeniomycetes, a taxonomic class of fungi that either parasitize arthropods or use them for dispersal, represent fungi and understudied taxa generally.

Knowing what we don’t know

While there will always be some things that scientists don’t know, taking stock of knowledge gaps, or “shortfalls,” is necessary to correct these blind spots and avoid unjustified certainty. To this end, Quandt and her co-researchers created a list of gaps in ecological knowledge, specifically those that can hinder conservation efforts. These four types of gaps are the Linnean, Wallacean, Latimerian, and Scottian shortfalls.

The Linnean shortfall, named after Carl Linnaeus, father of modern taxonomy, is the difference between the number of species that exist and those that scientists have described, Quandt says. While many species of macro-organisms, and some groups in particular (such as birds) have been discovered and described, this is not true of micro-organisms and groups like fungi. As to the shortfall’s significance for conservation, Quandt continues, species that are unknown cannot be conserved.

The Wallacean shortfall, named after Alfred Russel Wallace, a biologist who was an early proponent of the theory of evolution, has to do with incomplete information on species’ geographical distribution, according to Quandt. “The example from our paper is a species of Herpomyces [a genus of fungi] that we know from the Northeast, Panama and an area in eastern Africa.” Since these places are distant and apparently unrelated, it is unlikely that this species occurs only in those places.

The Latimerian shortfall, named after Marjorie Courtenay-Latimer, a naturalist who rediscovered a supposedly long-extinct fish, is expressed as the number of species in a taxonomic group that may or may not be extinct, “because they haven't been seen or recorded officially, or even unofficially in some cases, for 50 or more years,” Quandt says. Fifty years may seem like a long time for an existing species to go unobserved, but the fish Latimer documented was thought to have been extinct since the discovery of its fossils in the prior century.

Finally, the Scottian shortfall, named after Sir Peter Markham Scott, founder of the International Union for Conservation of Nature (IUCN) Red List of Threatened Species, is the difference between the number of described species in higher taxonomic groups (e.g., kingdom, phylum, class) and the number that have been assigned an IUCN classification. The IUCN is a global authority on the conservation status of various species, particularly via its Red List.

Why are some taxa understudied?

Laboulbeniales parasitic fungi growing on a Harmonia axyridis, or Asian ladybug. (Photo: Gilles San Martin)

There are several characteristics that make members of particular taxonomic groups difficult to study—they are often relatively uncommon, microscopic, lack distinctive form or do not grow in culture.

“There is a bias for scientists in general to describe things that are really common,” Quandt says. “So, things that many people are encountering on a regular basis get described sooner than rare taxa that you don't encounter that often.”

Of course, size plays into this, as does the lack of morphological traits: organisms the size of Laboulbeniomycetes will tend to go unnoticed even when they are encountered. For example, a fly agaric mushroom can be easily identified by its distinctive red-and-white cap, but the same is not true for the microscopic Laboulbeniomycetes.

The ability to grow cells in a cell culture—an artificial environment outside of a living organism—is similarly important, as it allows researchers to both manipulate and define the environment in which cells develop. This makes things that grow in culture easier to describe, Quandt says.

Another potential issue in poorly described taxa that Laboulbeniomycetes exemplifies is cryptic speciation. Cryptic speciation is when a new species forms without any traits that are clearly different from other species’.

Quandt gives an example: “The (study’s) first author, my former postdoc Danny Haelewaters, worked on one ladybug-associated taxon that people thought was one species because, morphologically, it looked like one thing; but when he was able to get samples from all over the globe, he used genetic data to separate them into separate clades, which he is now describing formally as individual species.”

There were morphological differences between the species, including size variation in some of their cells, but that sort of thing can be easily missed.

Knowledge shortfalls in Laboulbeniomycetes

In looking for the Linnean shortfall for Laboulbeniomycetes, the researchers first tried to use the class’ discovery curve data. Ideally, a discovery curve represents the gradually increasing number of discovered species within a group. However, this approach produced unrealistic results, likely because the species discovery curve data for Laboulbeniomycetes is flawed, as is typical in poorly studied taxa.

Laboulbeniales parasitic fungi growing on a Scaphidium quadrimaculatum, or shining fungus beetle. (Photo: Katja Schulz)

“One of the reasons that it's misleading for poorly studied taxa is because there are different rates of study for these groups,” Quandt says. For instance, certain specialist taxonomists may contribute significantly to the known number of species in a short time, creating a rapid increase in discoveries after several decades of little progress.

This “skewed specialist effect” isn’t the only problem with discovery curves of understudied taxa though, Quandt continues, since a species can become popular and receive a lot of study from different labs around the world. “This is like something my lab is working on: describing some new species related to the fungus that causes White Nose Syndrome of bats. Because that was just discovered in 2009, there has just been this exponential rise in the number of people studying it.”

So, while the lack of solid discovery curve data prevents a certain estimate of the Linnean shortfall, this proves the difficulty of creating conservation strategies for members of understudied taxa, as such strategies cannot be effectively applied to species that have not been found.

To examine the Wallacean shortfall, the researchers created a heatmap of reports of Laboulbeniomycetes species. This heatmap showed that the highest reported diversity existed in the United States, with several other unconnected hotspots around the world. Quandt says that this is likely the result of the geographical bias in field work and taxonomy toward North America and the northern hemisphere generally.

For example, many countries that have been characterized as megadiverse, such as Colombia and the Democratic Republic of the Congo, report very few species, and many in the southern hemisphere report zero. However, the presence of a single species in distant places without reports from intervening countries (e.g., Guatemala, Spain and Ukraine, but not in between) suggests a significant Wallacean shortfall.

This shortfall makes it hard to estimate a species’ range size, which is a major consideration in conservation assessments such as the Red List. It also interferes with the use of species distribution models, which are similarly important for conservation efforts targeting rare species.

The Latimerian shortfall for Laboulbeniomycetes was determined using species description dates and published records of species sightings. The researchers found that at least 71% of Laboulbeniomycetes species were not reliably observed after their initial description, and the last reliable observation was 50 or more years ago for 51% of species, compared to 1.7–3% for land-dwelling vertebrates.

The number of species that have not been seen for a long time is an issue for conservationists because it means that it is unknown whether these species are in danger of extinction or have already gone extinct.

As to the Scottian shortfall, not a single species of Laboulbeniomycetes has been assessed for the Red List. While less than 100%, the Scottian shortfall for all fungi is pronounced too, Quandt says, as “at the time we wrote this paper, there were only 625 Red List assessments for all fungi,” compared to 150,000 described fungal species, which is likely a vast underrepresentation according to an article in Fungal Diversity.

Stigmatomyces scaptomyzae fungi, a species of Laboulbeniomycetes, on a vinegar fly. (Photo: Katja Schulz)

This is important because the Red List is a significant tool for conservationists and, Quandt says, it is difficult to act to conserve a species if it hasn’t been assessed for its Red List status.

Addressing knowledge shortfalls

All of this raises the question of how gaps in scientists’ knowledge of microscopic and otherwise difficult-to-study species like Laboulbeniomycetes can be filled. Quandt and her research colleagues say that emerging technologies and trends in scientific data collection may help, and list several examples: DNA metabarcoding, environmental DNA analysis and citizen science.

“DNA metabarcoding is a way to use a barcode, which is a section of the DNA that is unique to a specific species, and sequence those regions of the DNA for all the organisms in that DNA sample,” Quandt explains. “So, if I took a gram of soil, and I extracted all the DNA from that soil, I could use the barcode to see which species of fungi are in that one gram of soil.”

Environmental DNA analysis is very similar, she continues, as it is also DNA that is sequenced from the environment. That “could be a gram of soil, it could be a leaf; but it's DNA that is not from a pure culture that we have in the lab, or from a fruiting body like a mushroom. It's a whole community of DNA from some environment.”

Both technologies could be useful for surveying understudied taxa, as their presence may not be immediately apparent but would show up in DNA analysis of soil or other places where they live.

Citizen science is a movement in which regular people help scientists by contributing data, Quandt says. One example of a citizen science platform is iNaturalist, whose website says that every user observation “can contribute to biodiversity science,” and that findings will be shared with a data infrastructure organization “to help scientists find and use your data.”

The data provided by citizen scientists are generally useful, but in particular might help correct the Wallacean and Latimerian shortfalls—at least in more easily observable species—as more people looking will yield more sightings, and these can be used to fill out information about a species’ geographical distribution and/or reduce uncertainty about whether it has gone extinct.

Most importantly, Quandt continues, “we're at an important moment in the fungal conservation movement. There's a lot of momentum right now, among my colleagues, to start pushing fungal conservation forward, and that's really different than when I started in the field 15 or more years ago.

“The big take home from this paper that we wrote is that we need to be mindful, as we have all this momentum towards trying to help push fungal conservation, that we don't leave behind some of these groups that are already understudied, and that we try to bring them in and help conserve them, and think about their conservation status, and also keep them in mind when we're talking about fungal conservation as a whole.”

Researchers Thomas Matthews, Joseph Wayman, Jonathan Cazabonne, Felix Heyman and Thomas Martin also contributed to this study.

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Top image: A Harmonia axyridis, or Asian ladybug, attacked by Laboulbeniales parasitic fungi (Photo: Gilles San Martin)

Fish on film: uncovering the environmental drivers of black spot syndrome

Rachel Sauer — Tue, 12 Nov 2024 17:18:32 +0000

Fish on film: uncovering the environmental drivers of black spot syndrome Rachel Sauer Tue, 11/12/2024 - 10:18

Blake Puscher

51�Թ�� researchers use a unique, noninvasive method to determine the environmental factors contributing to several symptoms among tropical fish

For many researchers in biology and other natural sciences, dissecting specimens may not be desirable, though it is often necessary. This is because dissection means killing the animal a researcher is trying to study—a big issue, especially if the species is experiencing population decline.

Over time, such concerns have led scientists to develop a number of non-invasive techniques, including video transects. This is a type of video recording used in marine biology, in which divers film along a line of fixed length and depth to record images for computer-assisted analysis, obtain permanent data that can be reassessed later and survey wider areas in shorter amounts of time.

51�Թ�� scientist Pieter Johnson and his research colleagues use a unique, noninvasive method to determine the environmental factors contributing to several symptoms among tropical fish.

A recently published study by Pieter Johnson, a 51�Թ�� professor of distinction in the Department of Ecology and Evolutionary Biology, and lead author Cheyenna de Wit of the University of Amsterdam, demonstrates the benefits of recording rather than dissecting specimens.

In their paper on black spot syndrome in ocean surgeonfish, the researchers use video transects to measure the severity of the disease among thousands of fish and identify the environmental factors contributing to its distribution.

What is black spot syndrome?

Black spot syndrome is a collection of several symptoms, the most prominent being the dermal lesions or spots for which the condition is named, according to Johnson. In many species, Johnson says, these lesions are black, “but in some species they’ll show up as white.” They form on the skin, scales and fins of fish.

The spots appear when the free-swimming, larval form of trematodes—commonly known as flukes, a type of parasitic flatworm—penetrate the skin of the fish and form cysts inside them. The distinctive coloration occurs when fish surround the cyst with melanin in response to the invasion, similar to the formation of pearls in oysters.

Relatively little is known about the genus of trematode that causes black spot syndrome, Scaphanocephalus. “Prior to us detecting it in 2017,” Johnson says, “it had never been reported from Caribbean fish. So, it was wholly undescribed from that area.” Much remains unknown about this trematode, including the type of snail that Scaphanocephalus infects before moving on to fish.

However, trematode infection is clearly very common in certain regions: In Johnson’s study, 70% of observed fish showed signs of infection, while a companion study of other Caribbean fish demonstrated both how high the parasite loads are in that region, and how many different fish species seem to be affected, according to Johnson.

As to the consequences of infection for fish, there is some evidence, Johnson says, that infected fish may graze less and have more trouble maintaining buoyancy. Researchers also hypothesize that they are more conspicuous to predators.

“One in particular, of course, is osprey, which are visual, fish-specialized predators that are looking for fish through the water,” Johnson says. “When these infected fish tend to flash or turn sideways, and you can see those black spots, it probably makes it a lot easier for the bird to detect them.”

If this hypothesis is true, black spot syndrome could bolster the numbers of the trematodes that cause it, as Johnson says osprey are their definitive host. That means these trematodes must enter the body of an osprey to reproduce. The transmission of the parasites is trophic, so they are passed along when infected fish are eaten.

Noninvasive methods

While black spot syndrome can have negative effects on infected fish, the most important consequences could be for reef ecosystems. According to Johnson, black spot syndrome has been increasingly prevalent in important herbivorous grazing fish in the Caribbean, such as surgeonfish and parrotfish.

Learn more

For more information on the complex lifecycles of digenetic trematodes, see this article about other research from CU involving the parasites.

“In tropical coral reef ecosystems,” Johnson explains, “surgeonfish and parrotfish, and other herbivores play a key role by grazing on algae.” Since infected fish are evidenced to graze less, and since they may be more likely to be eaten by osprey, the population of algae in the affected area can increase.

“Algae and coral are in a dynamic balance,” Johnson says, and if there is enough algal growth, “it can start to overwhelm and kill corals. So, in these areas, we try to keep those populations of surgeonfish and parrotfish as viable as possible, so that they can continue to regulate and graze down the algae.”

In fact, some studies have even said that grazing fish can help save coral reefs, with particular emphasis on parrotfish because the prior primary grazer in the Caribbean, spiny sea urchins, were killed off by disease in the 1980s. Also, trematode infection isn’t the only thing threatening surgeonfish and parrotfish populations, as they are popular catches for fisheries.

Because the fish being studied are ecologically important, it is particularly important to avoid interfering with their populations. Ordinarily, this is difficult, since dissection is the surest way to confirm a trematode infection—the parasites being clearly visible inside the fish’s bodies. In this case, though, the black spots characteristic of black spot syndrome allowed for a different approach: the video transect method.

To record as many surgeonfish as possible, and therefore provide an accurate estimate of how many fish were infected, SCUBA divers filmed at 35 sites along the coast of Curaçao, an island in the southern Caribbean. They recorded two and five meters below water for either 10 minutes or until 20 adult surgeonfish had been filmed.

An ocean surgeonfish with black spot syndrome. (Photo: Cheyenna de Wit)

Environmental factors

Besides determining that 70% of surgeonfish showed visible signs of black spot syndrome, Johnson and de Witt correlated different environmental factors with the severity of the syndrome, which they based on the average number of spots per fish.

One of the most significant effects the researchers observed arose from longitude—that is, the position of fish from east to west along the leeward (downwind) shore. Both the prevalence and intensity of black spot syndrome was lower toward the east and higher toward the west.

Johnson hypothesizes that this effect is caused by urban and industrial development, as the east end of Curaçao, where a portion of the research took place, is privately owned and less developed. The researchers observed the same association between development and infection intensity in Bonaire, the neighboring island.

The first component of the effect was wave intensity, which was negatively associated with infection intensity because the larval form of trematode that infects fish can’t swim well enough to overcome opposing tides. Wave energy is usually greatest at the eastern end of Curaçao, so this will have contributed to the lower intensity of infection at the east end.

The other components were positively associated with infection intensity. Nitrogen concentration increases with sewage and domestic runoff, which can contain nutrients and other pollutants. Nutrients can increase the population of trematode hosts, and pollutants can weaken the immune systems of fish that trematodes infect.

While fishing pressure can be either positively or negatively correlated with parasite abundance, Johnson says, this depends on the species involved. In the case of Scaphanocephalus, fishing pressure could increase abundance if it removed predatory fish from the environment, resulting in an increased snail population.

Student learning

51�Թ�� students also play an important role in this research. Undergraduates in the field course Coral Reef Ecology and Conservation (EBIO 4090, taught by Johnson) spend their fall semester learning about coral reefs and the factors that threaten them before traveling to Curaçao over winter break. During a week-long SCUBA expedition, students learn how to collect video transect data using the same methods Johnson and his research colleagues use and are contributing valuable data to the understanding of black spot syndrome. For the upcoming trip, students will be revisiting some of the same sites as in the study to assess how black spot severity has changed through time, particularly following recent warm water bleaching events that have killed many corals.

Since most of the factors composing the difference between the east and west ends come from human action, it is possible that the severity of black spot syndrome could be significantly reduced if the handling of runoff and/or fishing behavior were changed.

A unique methodology

One noteworthy part of the way Johnson and de Witt’s study was conducted is that, with the videos collected, the researchers had observers record the number of lesions on each fish. This is unique, as prior studies have simply noted whether lesions were present, leaving the severity of infection uncertain.

Moreover, methods like the one used in this study may help to solve the challenges that come with observing ocean life. “There's a lot of ocean out there and not a tremendous number of people to study it,” Johnson explains, “so I think approaches like this could be applied in other areas where we're detecting blackspot syndrome.” Photos are an especially useful way to study the ocean because they are easy for anyone to take thanks to digital technology, he adds. For this reason, community science platforms like iNaturalist can be used to aggregate a large amount of data.

“When people are on vacation, or they’re diving, or they’re swimming,” Johnson says, “they upload all of their observations and fish photos, and we’ve been using that to scan across large sections of the Caribbean and lots of different fish species; and now some of the undergrads in the lab are also extending that to look into parts of the Indo-Pacific and other regions of the world where Scaphanocephalus occurs.

“So, I think those kinds of approaches, video transects and these community science-uploaded images, together start to give a much bigger picture of patterns of infection over large geographic areas.”

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51�Թ�� researchers use a unique, noninvasive method to determine the environmental factors contributing to several symptoms among tropical fish.

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An ocean surgeonfish with black spot syndrome. (Photo: Cheyenna de Wit)

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