Researchers call on conservation genomics efforts to better engage with Indigenous communities and knowledge

Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign

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A gray wolf (Canis lupus) at Mission:Wolf Sanctuary in southern Colorado. Gray wolves remain endangered in most of the continental United States, especially the Mexican wolf subspecies (Canis lupus baileyi) which suffers from genetic bottlenecking.

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Credit: Jenny Thompson

Throughout human ecological history, we have played a variety of roles within ecosystems around the world. In this so-called Anthropocene era, genomic innovations have given us new and powerful ways to influence the environment and the countless species with whom we share the planet. In two new publications, a team of researchers is calling upon their scientific colleagues and society as a whole to approach the use of these tools with ethical deliberation, in consultation with Indigenous Peoples and with the goal of holistically supporting ecosystems.

Both publications were collaborative efforts that carry forward the goals of the Center for Indigenous Science at the Carl R. Woese Institute for Genomic Biology at the University of Illinois Urbana-Champaign. The first, published in Ethnobiology Letters, focused on strategic and ethical considerations of species “de-extinction” using genomic technologies. The second, appearing in Conservation Biology, explored broader concerns related to nonhuman genomic data use in conservation.

"The Center for Indigenous Science promotes ways to do science that extend beyond what has typically been seen in academic systems, specifically to Indigenous science systems,” said Alida de Flamingh, a postdoctoral scholar within the CIS. “This research promotes Indigenous data sovereignty, as well as access and benefit sharing.”

In the Conservation Biology publication, de Flamingh and her coauthors at the University of Illinois Urbana-Champaign and Oregon State University discussed the pressing importance of collaboration among Indigenous communities and conservation-focused research groups. They contrasted efforts to enact ethical guidelines for human genome research involving Indigenous communities, and the absence of any similar framework for nonhuman genome research.

“There's already a really phenomenal foundational set of work that has been done by Indigenous scholars and communities . . . that informs how to think about genomes in a culturally grounded way,” de Flamingh said. “That's informed my own thinking and also represents a large aspect of the research that we do in CIS that uses ancient DNA research on nonhuman organisms.”

The coauthors specifically consider biobanking, an emerging conservation genomics practice that involves collecting and storing biological samples or genomic data from a variety of organisms to allow their study and enable future restoration efforts. As technologies have emerged to rapidly sequence, analyze, and use DNA sequence from these beings, a societal consensus on how to most responsibly use these capabilities has not kept up. 

To ground nonhuman biobanking practices, the researchers recommend extending to the principles of respecting Indigenous data sovereignty and ensuring access and benefit sharing that are being established for human genomic and ancestry research. For example, Indigenous groups hold valuable knowledge about species of cultural and ecological importance that could be prioritized for biobanking; the paper describes key roles played by Indigenous communities in restoration efforts for the Great Barrier Reef, as well as for bison populations in the United States.

“People aren't often considering what constitutes a culturally significant species, or thinking about organisms . . . as being part of this relational kind of system that we live in,” de Flamingh said. “Relationality is a concept that we often talk about in the CIS and that also forms a part of Indigenous thinking about existence."

The importance of a more holistic view of ecosystems in conservation work was also emphasized in the Ethnobiology Letters article. Lead author August Hoffman and his colleagues in the CIS considered the specific example of last year’s announcement by Colossal Biosciences that the biotechnology company had “resurrected” the extinct dire wolf species through the use of genomic data and CRISPR gene editing technology.

“Colossal is ostensibly doing some more grounded ethical work with critically endangered red wolves, but that has taken a backseat to this glitz and glamour” of the dire wolf project, Hoffman said. “I would just want people to think about: there's a distinct reason why they chose dire wolves. It was logistically pragmatic and expedient, but you're also going to get a very different public reaction from resurrecting the dodo versus the dire wolf.”

Although the project was successful at capturing public attention, the researchers point out that it did not set a clear precedent for what an ecologically sound de-extinction effort might look like.

"We also aimed to bring attention to those individuals impacted by Colossal Biosciences's work, including Indigenous peoples who have been caretaking these ecosystems for millennia and the living, breathing animals who become caught up in project of ‘de-extinction,’’ said professor of anthropology and coauthor Amanda Cortez (CIS). “As biotech companies continue to develop these projects, we should forefront the individuals who are most impacted and continue moving toward collaboration with Indigenous communities that are heavily affected by ecological changes."

By making targeted edits to the genome of a gray wolf, the company succeeded in producing offspring with dire wolf traits, but the limited scope of the project could not encompass a consideration of the role dire wolves once played within the ecosystem or whether it could be possible for them to survive in the wild now.

“Even these definitions are very much in flux,” Hoffman said. “We're all kind of getting our wires crossed by speaking past each other, instead of asking what do we mean by de-extinction, resurrection, and what does it mean to be a being in a larger ecosystem?”

Hoffman and his coauthors, including de Flamingh, propose that in order to be employed ethically and responsibly, conservation efforts based in genomic technologies should consider ecosystems in a more holistic manner, and the roles of the species within them; focus on currently endangered species; and center Indigenous communities and knowledge.

In each case, conceiving and drafting the article was a truly collaborative process that reflected the ethos of the Center, with important contributions from CIS members: Oregon State University anthropology professor Alyssa Bader; Nathan Alexander, postdoctoral scholar with the Illinois Natural History Survey; Illinois professors of anthropology Ripan S. Malhi and Katelyn Bishop; American Indian Studies professor Jenny L. Davis; and Joshua Diaz, a doctoral candidate in anthropology at Illinois. 

“It was a really organic process,” Hoffman said. “It also was in practice, a representation of what the ethics of Indigenous science can do.”

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Journal

Conservation Biology

DOI

10.1111/cobi.70301 

Method of Research

Commentary/editorial

Subject of Research

Animals

Article Title

Considerations for biobanking of nonhuman genome data connected to Indigenous Peoples and lands

 

More Canadian than the beaver? Scientists discover a western toad found only in Canada

Study finds that Calling and Non-calling western toads differ genetically, behaviourally, and ecologically, with important implications for conservation.

University of Ottawa

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University of Ottawa study finds that Calling and Non-calling western toads differ genetically, behaviourally, and ecologically, with important implications for conservation.

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Credit: Jayna Bergman, University of Ottawa

The beaver and moose may be enduring symbols of Canadian wildlife, but neither is uniquely Canadian from a genetic perspective. But a team of researchers from the University of Ottawa have now discovered something rare, a genetically distinct and exclusively Canadian population of Western toad (Anaxyrus boreas). This discovery highlights our country’s unique biodiversity and has important implications for conservation and wildlife management.

Published in the journal Diversity and Distributions, the study dives into the genetics of the Western toad, which is widely found across North America, particularly in the United States and in the provinces of Alberta and British Colombia.

‘Calling’ and ‘Non-calling’ populations genetically distinct

Lead author Jayna Bergman and her team travelled through ponds, wetlands, and lakes across Alberta and BC collecting samples from toads and tadpoles for ancestry-type testing that compared the toads DNA to see how closely related they were.

They found that the previously designated Calling and Non-Calling Western toad populations are genetically distinct. Calling toads (east of the Canadian Rockies) have vocal sacs and make mating calls, whereas non-calling toads (west of the Canadian Rockies) lack vocal sacs and do not make mating calls.

The new genomic evidence shows these aren't just behavioral differences—they are also genetically different populations. Because DNA slowly changes over time, populations that have been separated for long periods accumulate small genetic differences. By measuring these differences, researchers could identify which animals belong to the same genetic group and which come from distinct groups.

“Our findings of a genetically distinct group entirely contained to a Canadian province is very unusual. These genetic results suggest we should be doing more to protect this species, especially the Alberta population of the Western Toad because of its unique complement of the species’ total genetic diversity,” says Bergman, a PhD student at the Faculty of Science and in Professor Julie Lee-Yaw’s lab.

Implications for conservation planning

Western toads, which are crucial to healthy ecosystems, are already designated as a Special Concern by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) and are listed under the Species at Risk Act.

Curiously, toads to the east of Canada’s Rocky Mountains have a vocal sac that produces a distinct mating call, whereas toads to the west of the Rockies and in southern parts of the species' range lack these traits.

“This ‘advertisement call’ provides a notable difference in breeding strategies and may be the only example of such an extreme difference in calls within what are considered the same species,” explains Assistant Professor Lee-Yaw, an Assistant Professor from the Department of Biology, highlighting the uniqueness in comparison to non-calling types which range from California to Alaska. There are also habitat differences between the toads that can play a part.

In Canada, wildlife protection decisions depend heavily on identifying distinct populations and look at genetic distinctions, behavioural distinctions and if they are barriers to gene flow. In this case, the mountains, and climate differences associated with them, appear to have helped keep the two groups of toads separate.

A second surprise discovery

The team made another intriguing discovery when they identified a third genetic group of western toads in the southern Canadian Rocky Mountains. This previously unrecognized  genetic group of toads is found in southeastern BC and southern Alberta and likely extends south into Montana in the USA. Many species in Canada were studied decades ago using limited genetic tools, but modern genomic techniques are helping identify previously unrecognized populations and evolutionary lineages.

Bergman says the next phase of this research should look to compare western toads across the entirety of their range to better understand how these distinct groups arose and whether the different genetic groups can successfully mate with each other—an essential step to testing whether they may be on the way to becoming different species.  

 

“Our findings of a genetically distinct group entirely contained to a Canadian province is very unusual. These genetic results suggest we should be doing more to protect this species, especially the Alberta population of the Western Toad because of its unique complement of the species’ total genetic diversity,” says Jayna Bergman, a PhD student at the Faculty of Science at the University of Ottawa.

Credit

Jayna Bergman, University of Ottawa

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Journal

Diversity and Distributions

DOI

10.1111/ddi.70219 

Method of Research

Meta-analysis

Subject of Research

Animals

Article Title

Pronounced Genetic Structure Associated with Differences in a Reproductive Trait and Climatic Barriers in Canadian Populations of the Western Toad (Anaxyrus boreas)

 

The other road to a mind

A small fish and a human, hundreds of millions of years apart, build the sensing brain by the same underlying logic. The finding suggests there may be rules a vertebrate brain follows.

Norwegian University of Science and Technology

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Zebrafish forebrain labelled for excitatory neurons in red and inhibitory neurons in green. Confocal image: Dr Stephanie Fore, Kavli Institute for Systems Neuroscience

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Credit: Dr Stephanie Fore, Kavli Institute for Systems Neuroscience

Line up the brains of a fish, bird and a mammal, and something unexpected comes up. You do not see three different answers to the problem of making sense of the world. You see one answer, tilted three different ways.

"You can really see it's almost like a continuum," says Emre Yaksi, a professor at the Kavli Institute for Systems Neuroscience in Trondheim. Read across decades of anatomy, the same two ancient pathways carry the world into the forebrain of all these animals. What changes from one to the next is mainly which route does more of the work. Evolution built these brains from different parts, in creatures that parted ways hundreds of millions of years ago. It kept arriving at the same answer anyway.

That is the puzzle the Yaksi lab set out to chase. If animals this far apart on the tree of life keep landing on the same arrangement, perhaps the arrangement is no accident. Perhaps there are organisational rules deep enough that a fish and a person, for all the differences between them, are bond by the same ones. The Yaksi lab’s new study, published in Science with Dr Anh-Tuan Trinh as the first author, is an attempt to catch one of those rules at work in the least likely animal there is.

The problem every brain must solve

Let’s start with what the brain is up against, because everything else follows from it.

Our perception of the world does not arrive whole: it comes in through separate senses. Light through our eyes, sounds and vibrations through others. Each pouring into our brains via on its own pathway. And yet you never experience a jumble of channels. You experience one seamless world. Somewhere inside, the brain has to take those separate streams and merge them back into a single scene. How does the brain arrange itself to manage that?

It helps to picture a house. The senses arrive at the door, and someone has to meet them and show each one where to go. In a mammal, that receptionist job falls to a structure called the thalamus. It receives the incoming senses and sends each to its own room, vision to one, sound to another, keeping them apart at first. Only deeper in the house, in the rooms we call the cortex, do the senses meet again, mingle and get compared, until somewhere in the innermost rooms they become thoughts, perceptions, decisions.

That layout, senses sorted at the entrance and combined in different ways deeper in, is one of the most dependable designs in vertebrate brain evolution. What Trinh, Yaksi and their co-authors wanted to know was whether a creature on a completely different branch of the family tree builds a similar house.

The room

To watch a brain do this, you first have to keep a fish still and content.

A young zebrafish, not yet three weeks old and less than a centimetre long, is settled into a bed of clear gel beneath a microscope. A small opening is made in the gel near its mouth, so fresh water can flow past and it can breathe easily. The fish is then acclimatised to this small, enclosed world, the way a person might be settled and reassured before an MRI scan.

Then there is the wall of instruments. "You activate a whole bunch of switches," he says. "It reminds me of the cockpit of an aeroplane, or a spaceship. There are so many buttons everywhere." He has spent years learning them. "It's like playing the piano. At first, it's very hard. Over time you get better."

What the buttons buy is something he has never stopped marvelling at. He first saw the activity of a living brain more than a decade ago, as a student. "The first time I saw neurons lighting up here and there, it was just like fireworks in the brain. It was so amazing." The fish offers something no mammal can. You do not see a small patch of brain, you see the whole of the forebrain at once, end to end, every neuron flaring the instant it fires, in an animal that is alive and sensing. The entire stage lit and behaving, in real time.

Sorting the world

The experiment itself was simple. Trinh showed the fish a flash of red light. He sent a faint buzz through the water. Sometimes one, sometimes the other, sometimes both together, and watched where the brain answered.

Each signal means something to a fish. A flash of light can be as ordinary as a shadow sliding past, a change in the surroundings worth noticing. The buzz is more pointed. Fish can sense movements in the water, and it is sensitive enough to feel the smallest vibrations. "If a predator comes towards a fish, there's a lot of water movement," Trinh says. The lab's gentle tremor is subtler than that, less an attack than an ambush. "It's really like a surprise signal. Like if somebody sneaks up and taps you on the back. That's the kind of signal we gave the fish."

When the team traced where these signals land, they found the fish keeps a different doorkeeper than we do. It is not the thalamus that meets the senses at the entrance, but another structure altogether, fed from the sensing centres of the midbrain. The researchers call it the PG, which is short for preglomerular complex. PG does the same tidy work. It takes the world in and passes it onward sorted, light towards one region of the forebrain, vibration towards another, each stream still clean and separate. The same first rooms, in a different house.

The cells that wait

But the fish's forebrain does not simply hand the senses along. It works on them, and the deeper Trinh looked, even stranger the cells became.

The plain, single-sense neurons gave way to cells that answered to both light and vibration, the two streams starting to merge. And then, further in, he found a type of neuron he had not been looking for. It stayed quiet when the light flashed on its own. It stayed quiet when the water trembled on its own. It woke only when the two came together at the same moment, and when it did, it fired harder than either event alone could account for.

Anyone who has stood outside in a storm knows the phenomena these cells are built around. The lightning reaches your eyes a moment before the thunder reaches your ears, and still, you know they both belong to the same event. You feel one storm. Something in your head binds the flash to the crack despite that delay. Here in a fish, the researchers caught cells doing exactly that, registering not the flash, not the crack, but the coincidence that the two arrived together.

Trinh found them not at the microscope but afterwards on his computer, deep in the analysis, and he did not believe them at first. "I was blown away. My first reaction was, is this real or not?" He spent the next few hours running the analysis every way he could think of, trying to make the pattern break. It would not. When he finally accepted it, he sat and did nothing useful for a while. "I literally spent ten minutes just looking at these beautiful plots."

What he was looking at was a kind of a hierarchy, ‘a ladder’ built across the brain. Towards the back sat the simple cells, each minding a single sense. Towards the front, the cells that combined and compared. Simple answers near the entrance. Stranger ones more difficult to predict the deeper you went. The same climb from sensing to perceiving that runs through our own cortex. What these front cells are finally for, no one yet knows. The team has watched what they do, not what they are used for, and nobody has yet tested how they shape the way the fish behaves. For now, they are neurons that seem to be built to notice when two things belong together, which is the very thing a brain has to manage before it can learn that one thing causes another.

Why a fish should bother

But why should a tiny zebrafish brain resemble ours at all?

Most of what keeps a mammal alive does not happen in the cortex. The cortex is not for chewing, moving or making babies, and it is not even needed to dodge an obstacle in its path. The forebrain is for the moments when the world stops behaving as expected: a moment where a creature has to find a new way through and when nothing pre-built could have prepared for it. And it seems that the pressure to build such a brain structure, a machine for adapting, pushes very different animals towards similar solutions.

This is where Yaksi reaches, of all things, for soup.

"You want to thicken your soup. You can put potatoes and rely on the starch, or you can put flour, and it also works. The solutions are similar, but you do not necessarily need to rely on the same material as long as it functions similarly. Two cooks, different ingredients, one result. Two vertebrate lineages, two different sets of brain parts, one design. Sort the senses, merge them room by room, add in cells that respond to a coincidence, and build upward from there.

Whether the fish inherited this arrangement from a shared ancestor, or arrived at it entirely on its own, is a question the lab is now chasing at the molecular level, comparing the cell types that build the circuit in the fish against those in the mammalian cortex and thalamus. It may turn out the two were assembled from the same raw materials after all. Or the fish may have found its own materials and still ended in the same place. Either way, it is the kind of finding that makes a scientist choose words with care. The fish's doorkeeper is not our thalamus in disguise, and whether the two share any ancient kinship is a question for work still to come. What the fish shows, plainly, is that the road matters less than where it leads.

The rule in the fish

There is an idea behind the work in Trondheim, that the brain runs on discoverable recipes, organising principles it follows the way a kitchen follows a method, and that if you look closely enough you can read them straight off the living tissue. This study catches one of those recipes in the unlikeliest place of all. Not in a primate, not even a mouse, but in the forebrain of a small, transparent fish.

"I don't argue that a fish has the equivalent of a mammalian cortex," Yaksi says. "But a fish has something. It's the pallium. And it evolved from the same vertebrate ancestors that our human cortices evolved from." Most of what it does is still in the dark for him, and he says so gladly. The study, he insists, only found the way in. "We just now learned where the world comes in. That is how everything starts."

But the way in, opens onto something large. If a fish and a person, hundreds of millions of years apart, both take the world in through separate pathways and then stitch it back together by the same logic, then that logic starts to look less like a ‘mammalian accident’ and more like a common rule. Something a brain arrives at again and again, because the task of making sense of a world leaves it little other choice.

A mind, it turns out, can be reached by more than one road. The roads keep ending in the same place.

Anh-Tuan Trinh, Anna Maria Ostenrath, Ignacio del Castillo-Berges, Fanchon Cachin, Mina Koç, Susanne Kraus, Bram Serneels, Koichi Kawakami and Emre Yaksi, “Hierarchical sensory processing in zebrafish thalamocortical-like circuits,” Science, 2 July 2026. https://doi.org/10.1126/science.aec2171

 

Zebrafish in the Yaksi lab. Photo: Kavli Institute for Systems Neuroscience

Journal

Science

DOI

10.1126/science.aec2171 

Method of Research

Experimental study

Subject of Research

Animals

Article Title

Hierarchical sensory processing in zebrafish thalamocortical-like circuits

Article Publication Date

2-Jul-2026

 

Scripps Research scientists awarded $2M to advance global disease surveillance

Two Gates Foundation grants will expand wastewater surveillance and AI-driven disease monitoring to support faster public health responses worldwide.

Scripps Research Institute

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Scripps Research Professor Kristian Andersen (far left), Dylan Pilz (second from left) and Senior Project Scientist Josh Levy (far right) with their NICD colleagues at a recent conference in Accra, Ghana.

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Credit: Scripps Research

LA JOLLA, CA—Detecting infectious disease threats early and responding quickly can dramatically alter the course of an infectious outbreak. Technologies such as wastewater surveillance are transforming how public health officials identify emerging pathogens, monitor community transmission and direct resources where they're needed most. Scripps Research has been at the forefront of this effort, developing computational and laboratory tools that have helped make wastewater disease tracking a reality for global health.  

Now, with two new grants from the Gates Foundation totaling $2 million, Scripps Research scientists will further expand these capabilities—developing more comprehensive wastewater surveillance technologies while building artificial intelligence systems to integrate diverse data and improve outbreak prediction. Both awards are part of the Modjadji Initiative, an effort to build affordable, scalable pathogen surveillance systems, particularly for low- and middle-income countries (LMICs). 

"We are very grateful to the Gates Foundation because these grants will allow us not only to expand the wastewater tools we've been developing, but also to use artificial intelligence to improve global health decision-making more broadly," says Josh Levy, a senior project scientist at Scripps Research and a leader on both projects. "By working closely with our partners around the world, we're creating systems that can help detect outbreaks earlier and support faster, more targeted responses."

One award renews a 2023 Gates Foundation grant, led by Scripps Research professor Kristian Andersen and Levy in collaboration with the National Institute for Communicable Diseases (NICD) in South Africa and the University of Birmingham in the United Kingdom.

The researchers will expand the computational and laboratory methods used for wastewater surveillance, enabling monitoring of a broader range of pathogens while reducing gaps that currently limit infectious disease tracking in many parts of the world, particularly in low-resource settings. The team will also adapt these tools for wastewater sources beyond traditional sewer systems, including for monitoring streams, canals and other surface waters that may be impacted by human wastewater.

Central to the project is Freyja, an open-source wastewater analysis platform developed by the Andersen lab that became a widely adopted tool during the COVID-19 pandemic. With the renewed award, Levy and colleagues will expand Freyja to detect additional infectious disease threats while optimizing both laboratory protocols and bioinformatics tools for use in LMICs. 

"Our goal is for the laboratory protocols, computational tools and resulting data to remain openly available so they can be used by researchers and public health agencies around the world," Levy says.

The second grant, led by Levy and institute investigator Karthik Gangavarapu, moves beyond disease detection to outbreak prediction. Researchers will develop AI and machine learning approaches that integrate multiple data types (testing and sequencing) as well as modalities (wastewater and clinical) into a unified picture of disease transmission. By combining these complementary data sources, the models will help fill surveillance holes and guide public health officials toward the most effective interventions.

The project will initially focus on South Africa and Zambia, where Scripps Research will partner with the Zambian National Public Health Institute (ZNPHI) alongside other collaborators that are part of the Modjadji Initiative.

Beyond strengthening preparedness for future pandemics, the work will expand monitoring for diseases such as measles and tuberculosis. In Zambia specifically, the integrated platform will help identify cholera transmission hotspots to better target clean water interventions and vaccination campaigns, while also improving understanding of community transmission risk for mpox.

"Bringing these different sources of information together is essential for responding to emerging threats, and to prepare for the threats we haven't seen yet," says Levy. "Every community has different risks and different health needs. By integrating these diverse data streams, we can build robust and scalable public health surveillance that provides more accurate and actionable data for decision-makers."

 

About Scripps Research

Scripps Research is an independent, nonprofit biomedical research institute ranked one of the most influential in the world for its impact on innovation by Nature Index. We are advancing human health through profound discoveries that address pressing medical concerns around the globe. Our drug discovery and development division, Calibr-Skaggs, works hand-in-hand with scientists across disciplines to bring new medicines to patients as quickly and efficiently as possible, while teams at Scripps Research Translational Institute harness genomics, digital medicine and cutting-edge informatics to understand individual health and render more effective healthcare. Scripps Research also trains the next generation of leading scientists at our Skaggs Graduate School, consistently named among the top 10 US programs for chemistry and biological sciences. Learn more at www.scripps.edu.