Navigating muddy waters: What the Gila chub teaches us about the evolving science of taxonomy

In June 2025, the U.S. Fish and Wildlife Service proposed removing the Gila chub, a species of warm-water fish native to the Lower Colorado River basin, from the Endangered Species list. More than two decades of conservation and management efforts have certainly helped protect the fish since it was originally listed in 2002 – but that isn’t the reason for the proposed removal.

As it turns out, the Gila chub may not be a species after all.

At least, it may not be a separate species. According to the U.S. Fish and Wildlife Service, there is substantial evidence that the Gila chub (Gila intermedia) has enough physical and genetic similarities to the roundtail chub (Gila robusta) and headwater chub (Gila nigra) that it does not meet the definition of a species under the Endangered Species Act. In essence, it appears that all three chubs are actually subspecies of a single species of fish.

“The chub species in question are actually a really interesting test case for our ability to decide exactly what should be considered a species,” said Jessica Rick, an assistant professor specializing in wildlife and biodiversity conservation and management in the School of Natural Resources and the Environment. “And it highlights the management implications of such a debate.”

The Gila chub’s species status – or lack thereof – has been controversial among biologists and taxonomists for years, and definitive conclusions have been hard to come by. But why? What determines whether or not something is a species?

Species classification: A history

You probably encountered our contemporary classification system in biology class: kingdom, phylum, class, order, family, genus, species. And because it was printed in textbooks and copied onto flashcards, you may have considered it as set in stone, that what determines whether an organism belongs to a certain species was settled science.

Not so, according to Scott A. Bonar, a professor in the School of Natural Resources and the Environment and unit leader of the Arizona Cooperative Fish and Wildlife Research Unit.

“The species concept has always been a tough one for biologists and taxonomists to tackle,” he said. “It’s important to realize that it’s something we humans invented. You’ve got all these organisms out there evolving at different rates and going in different directions – it’s a continuous thing. And we’re trying to sort things into static categories. So that’s your issue right there.”

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Rick explained that species have historically been delineated using a combination of physical traits (morphology), behavior and geographic location.

“Scientists would take measurements of a suite of different traits and statistically determine whether one group differed from another,” she said. “If the two groups differed enough, they were considered a different species.”

But that all started to change as DNA science advanced. Now, there was an argument that genetic difference should be a determining factor in species designation, rather than depending solely on observable physical and behavioral characteristics.

“In some cases, this results in scientists discovering new species that they didn’t know were different from one another based on how they look,” Rick said. “In other cases, scientists find that two groups that look like different species are actually just different ecotypes (individuals living in different habitats) or morphotypes (individuals that differ in a specific trait) within the same species.”

The latter case appears to have been what happened with the southwestern chubs (collectively referred to as the Gila robusta species complex). Based on morphology, the species complex was divided into three species, but recent papers using genetic data suggest that they may all belong to a single species.

Case closed, then? Not so fast. As with so much in science, it’s more complicated than that.

A murky debate

The debate over the Gila chub’s status goes back almost a century. It was first described in 1856, and it’s undergone numerous taxonomic placements since then. It was officially recognized as a distinct species in 1969, based on morphological features like number of fin rays, number of gill rakers, body shape, mouth position and scale patterns.

“Their distinctiveness from other chub species has been repeatedly debated, and the three species overlap in many of their morphological measurements,” Rick said.

Scientists tried to resolve the debate by using genetic data to prove whether there are significant genetic differences between the three species. A number of papers were published between 2015 and 2023 trying to settle the question through various genetic and genomic methods – and came to conflicting conclusions.

“What they found was that there were substantial genetic differences between fish in different watersheds, but not between species that had been designated as separate species based on their morphology,” Bonar explained. “So in other words, the genetics show us that there’s more genetic difference between the Gila chubs in two different watersheds than there is between Gila chubs and headwater chubs and roundtail chubs who are all from the same watershed. So the latest thought is that we need manage and protect individual watersheds rather than focusing on an individual species.”

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More than a name change

An accurate species designation matters to more than taxonomists. The downstream effects of a change in species designation include important management and conservation decisions that depend, in part, on the number of individuals that belong to a certain species.

Changes in classification methods will likely benefit giraffes, which as it turns out are actually four species, based in part on genetic differences. But if the Gila chub is collapsed into a single species along with the roundtail and headwater chubs, it may lose protections under the Endangered Species Act.

“Aquatic habitats throughout the Southwest are in decline,” said Christina Perez, a Tucson-based fisheries biologist at the Bureau of Land Management and CALES alum. “This decline is driven by multiple factors, including prolonged drought, excessive groundwater extraction, historical land use practices and invasive species. Consequently, aquatic organisms dependent on these rare and sensitive systems are also in decline.”

The Gila chub was first listed as endangered in 2002, and it has benefited from federal protections since then – and so have other species who share the same habitat. Perez noted that artificial habitats have been developed to provide refuge sites for endangered fish.

“In 2024 and 2025, the Arizona Game and Fish Department translocated over 100 Gila chub to Canoa Ranch Pond as a safe harbor site,” she said. “Such sites are essential to provide refuge populations a safeguard against potential events that could result in the local or regional extinction of wild lineages.”

Other projects include a collaboration between the Bureau of Land Management and Arizona Game and Fish to reintroduce beavers into Cienega Creek in fall 2025, which will improve existing habitat conditions for the fish and other native wildlife.

The U.S. Fish and Wildlife Service will decide on the question of the Gila chub’s endangered status in the coming months. But no matter what they decide, Bonar hopes the will to conserve the chubs and their habitat will remain strong.

“We can go back and forth and argue on what’s a species, or what’s a subspecies,” he said. “But the bottom line is that our native species – many of which are found nowhere else in the world – need to be protected and preserved.”