Ecology and Evolutionary Biology

Tree rings offer clues to small-population growth

Rachel Sauer — Thu, 05 Jun 2025 15:54:21 +0000

Tree rings offer clues to small-population growth Rachel Sauer Thu, 06/05/2025 - 09:54

Daniel Long

In a recently published paper, PhD student Ellen Waddle and her coauthors provide some clarity on a decades-old problem

When researching what drives the growth of small populations, ecologists consider several factors, says Ellen Waddle, a PhD student in the ��Ƶ’s Department of Ecology and Evolutionary Biology.

“There’s climate. There’s density, which can be thought of as both the total number of individuals in a population or how crowded or spread out individuals are. And then there’s stochasticity, which is this big word that just means variance” or random chance.

CU Boulder scientists Ellen Waddle (left), a PhD student in ecology and evolutionary biology, and Dan Doak (right), a professor of environmental studies, and their research colleagues found "that climate data alone did a pretty poor job of predicting population growth (in small tree populations)."

But whether any of these drivers matters more than the others is a question that has challenged researchers since at least the 1950s, and one that Waddle and her coauthors Mark R. Lesser, Christopher Steenbock and Dan Doak take up in a paper recently published in Ecology and Evolution.

Time and perspective

Researchers have tended to fall into opposing camps with this question, Waddle explains.

“There’s a lot of people that think if we can perfectly predict what the climate’s going to be in an area, we’re going to be able to perfectly predict how that population is going to grow through time. And then you have another set of ecologists that argue, well, it also really matters how many individuals you have in the population.”

Yet in their paper, Waddle and her coauthors come to a less divisive conclusion. By analyzing the rings of two long-lived tree species, Ponderosa pine and limber pine, “we found that climate data alone did a pretty poor job of predicting population growth. We needed to include other drivers (in our predictive models), like competitive density effects and stochasticity, to accurately reconstruct population dynamics over time.”

This means that no individual driver proved more influential than the others. They all mattered.

Which was somewhat surprising, Waddle says, considering the long timescale she and her colleagues were dealing with—many hundreds of years. (The oldest tree they sampled dates back to 1470, half a century before Queen Elizabeth I was born.)

“We're averaging over such a long timeframe that you might be tempted to think that random fluctuations and stochasticity are less important, but this sort of study highlights that that's not always true. There's a lot of uncertainty in how long it's going to take small populations to grow.”

“The most important aspect of our work, to my mind,” adds Doak, professor of environmental studies at CU Boulder and head of the Doak Lab, “is showing that simplifying assumptions we often make about population growth don’t seem to hold up.”

‘The entire history of a tree’s life’

Tree rings, says Waddle, are a gold standard for measuring a tree’s history, one with which most people are familiar. The center, or pith, signifies when the tree established, or secured its roots and became capable of growing on its own, and each concentric ring around it represents a year of growth.

CU Boulder researchers studied small populations of Ponderosa pine (seen here) and limber pine to better understand how drivers such as climate data and competitive density affect growth. (Photo: Wikimedia Commons)

But for their study, Waddle and her coauthors used tree rings—in the form of tree cores, or centimeter-wide rods extracted from living tree trunks—a little differently.

“What we did, which has not been done often, was to core every single tree in the population,” says Waddle, which enabled her and her coauthors to get a clearer picture of how tree populations changed over time than they would have gotten coring only a handful of trees.

“Another way to put it: The tree core data basically allows us to reconstruct annual censuses of population from start (1400s-1500s) through present day because we can know exactly how many individuals were alive in each year and when each individual first established.”

The tree-core samples themselves came from Bighorn Basin, a mountain-encircled plateau region in north-central Wyoming about 500 miles from Boulder. Waddle collected some of the tree cores herself in 2017, while an undergrad at CU, for what turned out to be her first camping experience.

Yet the bulk of the core samples owe their existence to Lesser and Steenbock. Lesser alone cored around 1,100 Ponderosa pines between 2007 and 2008, in hot, sometimes tense conditions.

“We (Lesser and an undergraduate field technician) would start hiking to the first trees of the day typically around 5 a.m. to avoid the worst of the heat,” Lesser recalls. “Trekking up dry streambeds to reach the trees we would encounter multiple rattlesnakes each morning and on one occasion a mountain lion that set us on edge for the rest of the day! Many days we would core fewer than 20 trees due to the low density of the population and the ruggedness of the terrain—getting from one tree to the next often took an hour or more negotiating cliff faces, ravines and steep slopes.”

But the effort, he says, was worth it.

“Coring the trees itself was an incredibly rewarding experience—sizing up the tree to get a sense of its shape and where the pith was and then extracting the entire history of its life!”

Pick a species, any species

This research on small-population growth is no small matter, says Doak, “because all populations start small,” and “understanding what controls the growth of new populations has a new urgency as we try to predict whether wild species can shift their ranges to keep up with climate change.”

“Pick some species you care about,” says Waddle, who is currently writing her dissertation on how mountain terrain affects plant species’ ability to follow their preferred climate. “What I care about might be different than what someone else cares about, but there’s probably a species that matters to you, whether it’s a food species or your favorite animal.

“If we want to help keep those populations on the landscape, we need to know how small populations grow and how they persist.”

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In a recently published paper, PhD student Ellen Waddle and her coauthors provide some clarity on a decades-old problem.

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You said a moth-ful

Rachel Sauer — Wed, 04 Jun 2025 16:09:34 +0000

You said a moth-ful Rachel Sauer Wed, 06/04/2025 - 10:09

Ryan St Laurent

It’s miller moth season in Colorado—an entomologist explains why they’re important and where they’re headed

It is spring on the Front Range of Colorado, which means before long the region will receive an influx of many, many moths.

Colorado is home to thousands of species of moths, many of which are hatching out from a winter of hibernation, known as diapause.

At night, porch lights, stadium lights and street lamps are regularly visited by moths, a collective term for most of the nocturnal members of the insect order called Lepidoptera. Butterflies are also part of this order, but they are mostly diurnal, or active during the day. Butterflies are actually just a subset of moths, so all butterflies are moths, but not all moths are butterflies.

Ryan St Laurent is a CU Boulder assistant professor of ecology and evolutionary biology and CU Museum curator of entomology.

The Front Range lies on the path of a springtime migration of a particularly familiar species of moth, usually referred to in this part of the country, including Colorado and neighboring states, as “miller moths.” Miller moth caterpillars are often called the “army cutworm,” a whimsical name referring to the caterpillars’ tendency to reach large numbers that march across fields and roads to find food. Both the moths and their caterpillars are rather drab and brown in color, though the moths are variable in patterning.

Many people find miller moths to be a nuisance, and the caterpillars can be a pest. But miller moths are a native species to Colorado and play important roles across the plains and up into the high country.

I am an assistant professor of ecology and evolutionary biology as well as the curator of the entomology collection at the University of Colorado’s Natural History Museum in Boulder. I study moths from around the world. I have a particular fascination for the large moth group known as Noctuoidea, the superfamily to which miller moths and their relatives belong.

As an entomologist, I crisscross the state looking for moths for my ongoing evolutionary, classification and life history studies. During miller moth migrations, they may swarm my moth traps, which are made up of a bright light in front of a white sheet. The crush of miller moths makes finding the less common species that I am looking for all the more challenging in a sea of dusty brown.

What makes miller moths so unique?

In temperate regions like most of North America, most moth species hibernate in the cold winter months. During this time, they are in a dormant pupal stage. Some species spin cocoons. They then hatch into adult moths, mate, lay eggs, and those caterpillars grow during the spring and summer. Come fall, the cycle starts over.

While miller moths also have a hibernation period, it is not like that of most moths. Miller moths instead spend their winters on the plains of eastern Colorado, Wyoming, Kansas, Nebraska and nearby states as partially grown caterpillars, rather than a pupa, having gotten a head start on feeding in the late summer. This puts the caterpillars at an advantage. As soon as the weather warms and low-lying crops like wheat and alfalfa produce new, nutrient-rich foliage during the early spring, the caterpillars are right there ready to feast and may cause serious damage to the crops in outbreak years.

Pupation then occurs later in the spring, and unlike in most Lepidoptera, the adult moths hatch without an extended pupal diapause, and instead begin to migrate west. They travel more than 100 miles (roughly 160 kilometers) toward higher elevations to seek out flowering plants, feeding on nectar and pollinating as they go.

To spot and trap moths, entomologists set up bright lights in front of a white background. (Photo: Ryan St Laurent)

This migration is where folks on the Front Range become all too familiar with these weary travelers, who seek out narrow spaces to rest, often crawling into gaps in cars and homes. Inside a home, miller moths don’t feed, reproduce or lay eggs. Sudden agitation of the resting moths may cause them to fly about to seek out a new spot to hide – that is, if your house cat doesn’t see them first. If they do make their way inside, they can be easily swept into a cup or jar and let outside.

People on the Front Range experience a second run-in with these moths after they finish their summer of feeding in the mountains and head back to the plains to lay their eggs in the fields from August to September.

The call of the night

The importance of pollinators is familiar to many Coloradans. The state offers many resources and groups to help create spaces to attract butterflies and bees, including an initiative that designated Interstate Highway 76 as the “Colorado Pollinator Highway.”

But pollination does not stop when the sun goes down. In fact, moths make up the largest percentage of pollinators in terms of number of species globally – more than bees and butterflies combined. But scientists have yet to figure out which plants miller moths pollinate.

Despite the importance of moths as pollinators to agriculture and ecology, by comparison to bees, for example, we know exceedingly little about nocturnal pollinators. Of the thousands of moth species in Colorado, many hundreds remain unknown to science. One of the reasons scientists study moths is to literally shed a light on these insects in the environment to see what they are doing.

My work aims to understand what certain moths eat in their caterpillar stage, but other researchers, and my colleague Dr. Julian Resasco, at the ��Ƶ, study what plants the adults are feeding on as they pollinate.

Colorado moths

Moths are among the primary airborne insects at night, playing a significant, and perhaps leading, role in insect-feeding bat diets. During their migration to the mountains, there are so many miller moths that they are a substantial protein- and fat-rich meal for animals as large as bears.

Considering that we still know so little about moths, it’s important to realize that light pollution, habitat loss and agricultural chemicals are all impacting moth numbers, resulting in annual declines in these insects globally.

So, the next time you see a miller moth in Colorado, or any moth at a light anywhere on Earth, remember that it’s working the night shift. Turn out that light so it can go about its way.

Ryan St Laurent is an assistant professor of ecology and evolutionary biology and CU Museum curator of entomology the at the ��Ƶ.

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

It’s miller moth season in Colorado—an entomologist explains why they’re important and where they’re headed.

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An apple a day? It’s the Boulder way

Rachel Sauer — Thu, 08 May 2025 17:18:27 +0000

An apple a day? It’s the Boulder way Rachel Sauer Thu, 05/08/2025 - 11:18

Rachel Sauer

Newly planted apple orchard on CU Boulder campus is a nexus of university and community partnerships and will be a living classroom for students and educators

For now, they are twiggy little things, all spindly adolescent limbs that nevertheless hint at future harvests. Saturday morning, one even wore a scattering of creamy white blossoms—flowers that, in years to come, once roots have gained hold and branches have stretched up and out, will grow into apples.

Is there anything more hopeful than planting a tree? Yes, planting a whole orchard of them.

On Saturday, years of planning, research and partnership-building bore fruit on an L-shaped plot in front of the ��Ƶ 30th Street greenhouse, where more than two-dozen volunteers planted 30 apple trees in what had previously been a scrubby patch of turf.

Funded by a $90,000 Sustainable CU grant, the apple orchard will not only be a classroom and a living lab, but a nexus for community, a carbon sink and a vibrant example that sustainability can be delicious.

“It’s so exciting to see this happening,” says Amy Dunbar-Wallis, who this semester completed her PhD in the Department of Ecology and Evolutionary Biology and collaborated with CU Boulder faculty and students and community partners to bring the idea of the first orchard on CU Boulder campus to fruition.

“It represents how so many people on campus, so many people in the community, have come together to plant this orchard that will be a place to learn and a place to preserve a really neat part of Boulder’s history.”

In search of old apple trees

The new apple orchard grew from the Boulder Apple Tree Project, an initiative that began almost 15 years ago with a simple observation: There seemed to be a lot of old apple trees in Boulder.

Katharine Suding, a professor of distinction in the Department of Ecology and Evolutionary Biology, had recently moved to the area, “and I was really surprised to see so many old apple trees everywhere,” she recalled during the 2022 Apple Symposium. “I realized I had no idea about the histories and particularly the history of apples, so looking into it a little more, it was clear there are trees here that are remnants of past histories starting in the turn of (20th) century.

Amy Dunbar-Wallis (left) and Tiffany Willis (right, EBio'22) consult a chart designating where each tree would be planted in the new apple orchard in front of the 30th Street greenhouse Saturday morning. Willis, who lives in Boulder, took EBIO 1250 online during Covid lockdowns and was a lab assistant for the class in 2021.

“There are apple trees in Colorado and in Boulder that are remnants from old orchards that still exist. There are also remnants of trees that were planted when people came and built ranches or had farms here, and often they were bringing along apple trees from where they came from, whether it was Germany, whether it was the Midwest, whether it was Scandinavia.”

In fall 2017, the Boulder Apple Tree Project (BATP) sprouted, combining historical sleuthing with cutting-edge genetic testing and grafting to not only locate and catalog Boulder’s historic apple trees, but also to revive its legacy of apple growing. In the ongoing project, researchers gather data on the age and health of the trees, as well as the type and flavor of the apples, and the genetic diversity that the trees offer to future populations.

Suding and BATP co-principal investigator Lisa Corwin, an associate professor of ecology and evolutionary biology, have worked with undergraduate and graduate students not only to gather data, but also to develop the EBIO 1250 course, during which students conduct research on Boulder’s apple trees; curricula and materials in partnership with the CU Museum of Natural History; a database and app in collaboration with computer science students; an interactive map of apple trees that have been tagged and studied; and the A Power of Place Learning Experience and Research Network (APPLE R Net), a multi-institution research network directed by Corwin that introduces students to field research by involving them in a project examining apple trees across the Rocky Mountain region.

BATP also is part of the Historic Fruit Tree Working Group, which connects Colorado researchers with other apple-exploring groups and researchers across North America.

Mia Williams (left) waters a newly planted apple tree Saturday morning. Williams, who will graduate this summer, is double majoring in ecology and evolutionary biology and environmental studies.

“This project has grown so much since our initial community engaged Apple Blitz in 2018,” says Dunbar-Wallis. “We've tagged over 1,000 trees and created a database, taught multiple course-based undergraduate research experiences at CU and at colleges across Colorado and northern New Mexico, started a data-collection app and interactive map in collaboration with CU computer science capstone students and installed a demonstration orchard in collaboration with Boulder Open Space and Mountain Parks.”

The demonstration orchard, planted two years ago, functions as a teaching and research laboratory to explore how biodiversity affects the functioning of apple orchards and their services to human well-being, including efficient water use, pollinator habitat and structural complexity supporting natural pest control.

A part of the narrative

The idea for the 30th Street orchard was revived by a group of six undergraduate and two graduate students almost two years ago, who proposed resubmitting a grant application that hadn’t been accepted in 2019.

“We’re a group who really love what we do and love apple trees and working with the soil,” says Katie Mikell, an ecology and evolutionary biology student who is graduating today and who was a member of the team that crafted and submitted the grant proposal.

“Before, (the orchard plot) was a lawn full of monoculture turf grass, so part of our argument was that if we put in an apple orchard, it would create a carbon sink (a system that absorbs more carbon than it releases), it would save the school money and anyone walking by could pick an apple. Plus, once the trees are producing, we can donate apples to the food pantry. Everyone can benefit from an apple orchard.”

Deidre Jaeger (right, PhDEBio'22) and her sons Sage, 4 (left), and Cedar, 1 (center), plant apple trees at the 30th Street orchard Saturday morning. Jaeger was a postdoctoral researcher in the Department of Ecology and Evolutionary Biology and an advisor for the Center for Sustainable Landscapes and Communities and is a researcher with the Boulder Apple Tree Project.

Students prepared the 30th Street site during fall semester, working with departments and organizations across the university, as well as many community partners. The trees planted Saturday are about three years old and were obtained from Widespread Malus and Benevolence Orchard in Boulder.

“Our students are at the core of the university, and their passion and ingenuity are critical to our values around infusing sustainability throughout CU Boulder. This orchard exemplifies that pursuit in so many ways,” says Vice Chancellor for Sustainability Andrew Mayock.

“It is not only helping to protect biodiversity in our community. It will help feed those in need on our campus and create a living-learning laboratory space where sustainability leaders of the future will learn and develop strategies for urban agriculture planning.”

Fifteen varieties of apples are represented in the orchard, including locally grown historic cultivars like Wolf River and Colorado Orange. A beloved apple tree on the Bobolink Trail is even represented in a newly planted graft.

“There’s so much learning that can happen in an orchard,” says Manuela Mejia, an ecology and evolutionary biology PhD student who will conduct her doctoral research, which will include studying insect diversity, at the orchard. “So many facets of science are represented here.”

In addition to trees, the orchard will include an understory of native, drought-tolerant grasses and pollinator-friendly wildflowers, notes Mia Williams, who is majoring in environmental studies and ecology and evolutionary biology and will graduate this summer.

“It’s really exciting that this orchard will become a part of the story of agriculture in this area,” Dunbar-Wallis says. “We’ve tagged more than 1,000 trees (through BATP) and some of them are a hundred years old, so you think about everything they’ve seen and been through, the history that they hold, their stories, and now these trees—which are little now and probably won’t produce fruit for two or three years—are part of that narrative.”

Sophie Small (left) and Amy Dunbar-Wallis (right) fill a wheelbarrow with compost Saturday morning to prepare for planting an apple orchard in front of the 30th Street greenhouse. Small, a freshman who is studying biomedical engineering, learned about the project through the CU Farm and Garden Club.

Sophie Small (left), Isaac Kou (center) and Kyrie MacArthur dig a hole Saturday morning before planting an apple tree in it. Small is studying biomedical engineering, Kou just graduated with a major in computer science and a minor in ecology and evolutionary biology and MacArthur is studying history and education.

Amy Dunbar-Wallis (PhDEBio'25) digs a hole for a young apple tree Saturday morning.

Amy Dunbar Wallis (left, black vest) educates student and community volunteers Saturday morning before they plant 30 apple trees in front of the 30th Street greenhouse.

The apple trees planted in the 30th Street orchard Saturday morning, one of which even bloomed, are three years old and should begin producing fruit in two or three years.

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Newly planted apple orchard on CU Boulder campus is a nexus of university and community partnerships and will be a living classroom for students and educators.

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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 ��Ƶ, 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.

CU Boulder 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 Boulder, 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/CU Boulder)

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 ��Ƶ 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 CU Boulder 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 CU Boulder 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

CU Boulder 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 CU Boulder 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 ��Ƶ 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 Boulder.”

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.”

CU Boulder 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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CU Boulder 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, CU Boulder 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 CU Boulder 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 CU Boulder 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.

"Would any one person living today have come up with Newton’s Laws of Motion? With Darwin’s theory of evolution by natural selection? It is not clear," notes Iskra Fileva, CU Boulder associate professor of philosophy. (Charles Darwin seen here in an 1881 portrait. 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, CU Boulder 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

CU Boulder distinguished professor recognized for ‘transformative contributions to restoration ecology’

Katharine Suding, a ��Ƶ 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 CU Boulder 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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CU Boulder 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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Apparently, herbivores are not fond of chewing sandpaper.

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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 CU Boulder 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 ��Ƶ 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 CU Boulder. 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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How a team of CU Boulder PhD students produced the first chromosome-level reference genome for humpback whales.

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

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