October | 2025 | College of Science

Dataset tracks ecological traits for 11K birds

October 3, 2025

Çağan Şekercioğlu

With the help of countless students and volunteers, the University of Utah conservation biologist has finally released BIRDBASE, an encyclopedic dataset of traits covering all the bird species recognized by the world’s four major avian taxonomies.

Described this week in a study published in the journal Scientific Data, the dataset covers 78 ecological traits, including conservation status, for 11,589 species of birds in 254 families. The main trait categories tracked are body mass; habitat; diet; nest type; clutch size; life history; elevational range; and movement strategy, that is whether and how they migrate.

While some little-known species still have incomplete data, the dataset provides a foundation for ornithologists around the world to conduct new global analyses in ornithology, conservation biology and macroecology, including the links between bird species’ ecological traits and their risk of extinction, according to Şekercioğlu, a professor in the university’s School of Biological Sciences. He also hopes BIRDBASE will help other biologists win support for studying avian conservation.

“To get funding you have to have a big question, but without data, how are you going to answer those big questions?” Şekercioğlu posed. “It also shows we still have ways to go. Birds are the best-known class of organism, but even though they are the best known, we still have big data gaps.”

BIRDBASE’s public launch coincides with the release of the first unified global checklist for birds, known as AviList, a grand taxonomy under one cover.

The BIRDBASE project started in 1999 when Şekercioğlu was a graduate student at Stanford University, spending field seasons in Costa Rica. While writing the first chapter of his Ph.D. thesis, he needed to know the percentage of tropical forest understory bug-eating birds, technically known as insectivores, that are threatened with extinction. He was perplexed to discover that information had yet to be determined.

Variation in seven example traits provided in BIRDBASE. Bars indicate the number of species within categories or subsets of each trait: (A) average body mass, (B) primary habitat, (C) primary diet, (D) nest type, (E) maximum clutch size, (F) elevational range, and (G) movement strategy. Example species (from left to right, top to bottom) include: Bee Hummingbird, Common Ostrich, Keel-billed Toucan, Cream-coloured Courser, Rainbow Bee-eater, Bearded Vulture, Chinese Blackbird, Malleefowl, Adelie Penguin, Northern Bobwhite, Horned Lark, and Snowy Albatross. Graphic credit: Çağan Şekercioğlu.

“I realized that statistic doesn’t exist because nobody had analyzed all the birds of the world and their threat status based on diet,” he said. “I’m like, this is unbelievable. There’s no global database on birds. I’m lucky that I was in grad school because I was naive and I love birds.”

In other words, he set out to figure it out himself. That meant gathering and organizing life history traits for all such bird species, including their diets, habitats and conservation status. For a keen birder like Şekercioğlu, it seemed like a simple task that would be fun, compiling data found on thousands of bird species published in huge beautifully illustrated volumes. It turned out to be tedious and seriously time consuming, but worthwhile.

Thanks to a cadre of volunteers in the Stanford Volunteer Program and undergraduates, whose labors were compensated by the Stanford Center for Conservation Biology, Şekercioğlu answered his question within a couple years. Twenty-seven percent of tropical understory insectivores were threatened or near threatened with extinction. This finding wound up not supporting the hypothesis of his research, but that’s science.

Yet the dataset was so helpful that he labored on with the data-compiling project to eventually cover all bird species and expanded the number of traits included. “What started as this little specialized question turned into this global database, the first of its kind” he said.

BIRDBASE has proven a boon to many other avian researchers who have tapped it to support dozens of papers, most of them listing Şekercioğlu as co-author. The tally of Şekercioğlu’s papers that have used BIRDBASE currently stands at 98, accounting for 14,000 of Şekercioğlu’s 24,000-plus citations.

Among the conclusions the dataset has enabled is that a majority of the world’s bird species, or 54%, are insectivores, and many species in this group are under pressure.

“Most of them are tropical forest species. It is a very important group and they’re declining,” he said. “They’re sensitive even though they’re not hunted. They are small, so they don’t need a big area. You wouldn’t expect them to be the most sensitive group to habitat fragmentation but they are highly specialized.”

The dataset also showed that fish-eating seabirds are at elevated risk of extinction as well, and fruit-eating birds are vital to the survival of tropical rain forests.

Broad-billed Tody, Dominican Republic. Photo credit: Çağan Şekercioğlu

“The most important seed dispersers in the tropics are frugivorous birds,” Şekercioğlu said. “In some tropical forests, over 90% of all woody plants’ seeds are dispersed by fruit-eating birds who eat them and then defecate the seeds somewhere else and they germinate.”

Now for the first time BIRDBASE is publicly available to all researchers online, “no strings attached.” It can be found as an Excel spreadsheet on a site hosted by Figshare, with separate worksheet tabs for trait values, trait definitions, nest details and data sources, packaged on one row per species.

Şekercioğlu emphasized that BIRDBASE remains a work in progress that will be continuously updated. Kind of like a medieval cathedral that is open for worship, but never really finished. He estimated that nearly 30 person-years of labor have gone into the project, work that entails entering data collected from various authoritative sources, such as BirdLife International, Birds of the World, hundreds of bird books and ornithological papers, and Şekercioğlu’s field observations of more than 9,400 bird species.

“Thanks to my being naïve, something that started with just a little question in grad school led to the foundation of my career. Right now, if one of my students came to me and said, ‘Hey, as part of my PhD I want to enter the world’s birds into a dataset,’ I’m like, ‘No, you’re not doing that. You’ll never finish your Ph.D.’ Fortunately I finished my Ph.D., but think about it, 1999 is when I had the idea and we are still putting finishing touches in 2025.”

by Brian Maffly
This story originally appeared in @The U.

The study, titled “BIRDBASE: A Global Dataset of Avian Biogeography, Conservation, Ecology and Life History Traits,” appeared Sept. 30 in Scientific Data, published by Springer Nature. Co-authors include current and former graduate students and lab members Kyle Kittelberger, Flavio Mota, Amy Buxton, Nikolas Orton, Adara DeNiro, Evan Buechley, Joshua Horns, J. David Blount, Jason Socci and Montague Neate-Clegg.

Stories about past research findings based on BIRDBASE data:

“Alien” bird invasions

Discovering the traits of extinct birds

Çağan Şekercioğlu’s Frontiers of Science presentation in 2017, “Why Birds Matter.”

Could a fungus provide a blueprint for next-gen hydrogels?

October 3, 2025

Fungi are vital to natural ecosystems by breaking down dead organic material and cycling it back into the environment as nutrients. But new research from the University of Utah finds one species, Marquandomyces marquandii, a ubiquitous soil mold, shows promise as a potential building block for new biomedical materials.

In recent years, scientists have examined fungal mycelium, the network of root-like threads—or hyphae—that penetrate soils, wood and other nutrient-bearing substrate, in search of materials with structural properties that could be useful for human purposes, particularly construction.

In a series of lab demonstrations, U mechanical engineering researchers and biologists show M. marquandii can grow into hydrogels, materials that hold lots of water and mimic the softness and flexibility of human tissues, according to a recent study.

Unlike other fungi that struggle with water retention and durability, M. marquandii produces thick, multilayered hydrogels that can absorb up to 83% water and bounce back after being stretched or stressed, according to Atul Agrawal, the lead author of the study. These properties make it a good candidate for biomedical uses such as tissue regeneration, scaffolds for growing cells or even flexible, wearable devices.

“What you are seeing here is a hydrogel with multilayers,” said Agrawal, holding a glass flask containing a fungal colony growing in a yellowish liquid medium. “It’s visible to the naked eye, and these multiple layers have different porosity. So the top layer has about 40% porosity, and then there are alternating bands of 90% porosity and 70% porosity.”

Looking to nature to innovate materials

Bryn Dentinger

Agrawal is a Ph.D. candidate at the John and Marcia Price College of Engineering. His paper is the latest to emerge from the lab of senior author Steven Naleway, an associate professor of mechanical engineering who explores biological substances to develop bioinspired materials with structural and medical applications.

Agrawal and Naleway are seeking patent protection for their discoveries about the Marquandomyces fungus.

“This one in particular was able to grow these big, beefy mycelial layers, which is what we are interested in. Mycelium is made primarily out of chitin, which is similar to what’s in seashells and insect exoskeletons. It’s biocompatible, but also it’s this highly spongy tissue,” said Naleway, whose lab is funded by the National Science Foundation. “In theory, you could use it as a template for biomedical applications or you could try to mineralize it and create a bone scaffolding.”

Fungi comprise its own kingdom of organisms, with an estimated 2.2 to 3.8 million species, and just 4% have been characterized by scientists. For decades, scientists have derived from fungi numerous pharmacological substances, from penicillin to LSD. Naleway is among a cohort of engineers now looking to fungal microstructures for potential use in other arenas.

Why fungal mycelia have interesting mechanical properties

In collaboration with U mycologist Bryn Dentinger, Naleway’s lab has produced a string of papers documenting potentially useful structural properties of various species of fungi. One outlined how fungi that grow short hyphae are more stiff than those that grow longer hyphae. Another catalogued the various ways bracket fungi’s high strength-to-weight ratios make them a viable alternative in various applications, including aerospace and agriculture.

The way fungal hyphae grow is the reason why mycelia could have useful structural properties.

A novel high-speed, high-def hyperspectral video camera

October 2, 2025

Rajesh Menon

This process is slow, however, meaning that hyperspectral cameras can only take still images, or videos with very low frame rates, or frames per second (fps). But what if a high-fps video camera could capture dozens of wavelengths at once, revealing details invisible to the naked eye?

Now, researchers at the University of Utah’s John and Marcia Price College of Engineering and College of Science have developed a new way of taking a high-definition snapshot that encodes spectral data into images, much like a traditional camera encodes color. Instead of a filter that divides light into three color channels, their specialized filter divides it into 25. Each pixel stores compressed spectral information along with its spatial information, which computer algorithms can later reconstruct into a “cube” of 25 separate images—each representing a distinct slice of the visible spectrum.

This instantaneous encoding enables the researchers’ camera system—small enough to fit into a cellphone—to take high-definition video, and the compressed nature of the component images opens up new real-world applications.

Fernando Guevara Vasquez

A study demonstrating the camera was led by research assistant professor Apratim Majumder and professor Rajesh Menon, both in the Department of Electrical & Computer Engineering. Coauthors include Fernando Guevara Vasquez, a U professor of mathematics. Funded by the Office of Naval Research, this research was conducted in collaboration with the U tech startup Lumos Imaging, which Menon and Guevara Vasquez founded in 2015.

The results are reported in the journal Optica.

The camera’s design represents a leap forward in how spectral data can be captured.

“We introduce a compact camera that captures both color and fine spectral details in a single snapshot, producing a ‘spectral fingerprint’ for every pixel,” Menon said.

Hyperspectral cameras have long been used in agriculture, astronomy and medicine, where subtle differences in color can make a big difference. But these cameras have historically been bulky, expensive and limited to still images.

“When we started out on this research, our intention was to demonstrate a compact, fast, megapixel resolution hyperspectral camera, able to record highly compressed spatial-spectral information from scenes at video-rates, which did not exist,” Majumder said.

The U team’s breakthrough lies in how it captures and processes the data. The key component is a diffractive element that is placed directly over the camera’s sensor. It’s the element’s repeating nanoscale patterns that diffract incoming light and encodes both spatial and spectral information for each pixel on the sensor. By encoding the scene into a single, compact two-dimensional image rather than a massive three-dimensional data cube, the camera makes hyperspectral imaging faster and more efficient.

“One of the primary advantages of our camera is its ability to capture the spatial-spectral information in a highly compressed two-dimensional image instead of a three-dimensional data cube and use sophisticated computer algorithms to extract the full data cube at a later point,” Majumder explained. “This allows for fast, highly compressed data capture.”

Instead of a filter that divides light into three color channels, the University of Utah engineers and mathematicians have developed a diffractive element that divides it into 25.

The researchers’ diffractive element contains a repeating pattern of nanoscale features.

Guevara Vasquez, of the Mathematics Department, modeled and designed the diffractive filter array and co-designed, with co-author Fernando Gonzalez del Cueto, the algorithm to reconstruct the hyperspectral images from the raw data captured by the sensor.

The camera’s streamlined approach also cuts costs dramatically.

“Our camera costs many times less, is very compact and captures data much faster than most available commercial hyperspectral cameras,” Majumder said. “We have also shown the ability to post-process the data as per the need of the application and implement different classifiers suited to different fields such as agriculture, astronomy and bio-imaging.”

Data storage is another advantage.

“Satellites would have trouble beaming down full image cubes, but since we extract the cubes in post-processing, the original files are much smaller,” Majumder added.

To demonstrate the camera’s capabilities, the researchers tried three real-world applications: telling different types of tissue apart in a surgical scene; predicting the age of strawberries as they decayed over time; and mimicking a series of spectral filters that are used in astronomy.

The current prototype takes images at just over one megapixel in size and can break them down into 25 separate wavelengths across the spectrum. But the team is already working on improvements.

“This work demonstrates a first snapshot megapixel hyperspectral camera,” Majumder said. “Next, we are developing a more improved version of the camera that will allow us to capture images at a larger image size and an increased number of wavelength channels, while also making the nano-structured diffractive element much simpler in design.”

By making hyperspectral imaging cheaper, faster and more compact, the U engineers have opened the door for technologies that could change the way we see the world and uncover details hidden across the spectrum.

College of Science

Month: October 2025

Dataset tracks ecological traits for 11K birds

Dataset tracks ecological traits for 11K birds

Çağan Şekercioğlu was an ambitious, but perhaps naive graduate student when, 26 years ago, he embarked on a simple data-compilation project that would soon evolve into a massive career-defining achievement.

Could a fungus provide a blueprint for next-gen hydrogels?

Could a fungus provide a blueprint for next-gen hydrogels?

Looking to nature to innovate materials

Why fungal mycelia have interesting mechanical properties

A novel high-speed, high-def hyperspectral video camera

A novel high-speed, high-def hyperspectral video camera

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