What's in a species? For suckers, some lines are blurred

Klamath largescale (Catostomus snyderi, called Yen by the Klamath Tribes) and Klamath smallscale (Catostomus rimiculus) suckers could be thought of as the river counterparts to lake-dwelling C’waam (Deltistes luxatus) and Koptu (Chastmisties brevirostris). They’re not listed under the Endangered Species Act, but scientists think their populations in the Basin have seen declines similar to their listed cousins. All four fish have similar physical characteristics, though they have adapted to living in different areas and spawning at slightly different times.

Josh Rasmussen, Klamath sucker program coordinator for the U.S. Fish and Wildlife Service, said that geographic and temporal separation is what divides the Basin’s sucker population into separate species. If they don’t spawn at the same time, there’s little chance of them mixing genetic material and giving rise to offspring with physical and behavioral characteristics of multiple species. But as the fish’s habitats have changed, Rasmussen said, hybridization has become more common in recent years.

“As you have this back and forth of isolation, it kind of makes the picture a little difficult to really tease out,” he said.

Previous research has found that recent droughts and water management actions in the Basin have pushed the two Catostomus species and the lake suckers closer together. C’waam and Koptu typically head into the rivers to spawn during April and May, roughly a month later than their river-dwelling cousins.

Other lake suckers in the Great Basin have hybridized in response to human activity, like the June and Utah suckers, which began spawning together after settlers altered the hydrology of Utah Lake. It only takes a few individuals overlapping their spawning with another species to produce hybrid offspring.

“It doesn’t have to be the whole population spawning on top of each other,” Rasmussen said. “It could just be a couple of weirdos.”

Many decades of spawning by those weirdos have turned the Klamath Basin’s genetic landscape of suckers into a tangled mess. Matt Smith, a fish biologist at the U.S. Fish and Wildlife Service’s Abernathy Fish Technology Center in southwest Washington, is working on the latest effort to unravel it.

Presented at the Service-hosted Sucker Symposium earlier this month, Smith’s research used the latest genomic technology to determine where in the Basin the four species overlapped genetically. Though a full data analysis has yet to be completed, Smith said his findings so far support previous studies that found no detectable genetic difference between shortnose and largescale suckers in the Lost River Basin.

That’s despite often-clear differences between the two species’ morphology and habitat. For example, largescale suckers, adapted to riverbed feeding, tend to have fleshier lips than shortnose suckers, who have adapted to feeding on algae and invertebrates in lakebeds.

Smith and his colleagues, including researchers at a genetics lab at the University of California Davis, used a relatively new technology called restriction site associated DNA (RAD) sequencing to analyze the genomes of about 700 fish, samples from whom had been taken over the past three decades.

Instead of using significant energy and time to scan a fish’s entire genome, the RAD technique compiles representative fragments that are easier for a computer to digest. Researchers aligned these fragments to reconstruct an abbreviated genome for each species and sequenced individual samples against it.

Sucker samples were taken from the Upper Klamath Lake watershed, the Upper Williamson River, the Klamath River below Lake Ewauna and the Lost River Basin. Smallscale suckers, which are the only species not endemic to the Klamath Basin, also had some samples taken from the Rogue River. Smith said part of the study’s purpose was to identify genetic markers that researchers could use to cross reference species in the field, allowing them to be more sure about which species of sucker they collect.

“Our results were the same as previous genetic work in that it’s fairly easy to differentiate Lost River and shortnose, but it was still a little bit complicated for shortnose and largescale,” Smith said.

That difference wasn’t evident on a genetic level for the two species in the Lost River Basin. However, unlike previous research, the study was able to find genetic markers that could differentiate between them in the Upper Klamath Lake drainage basin. Smith said that could be helpful to field researchers identifying specimens in that area.

“This research looks promising for the ability to not only differentiate those two species but also identify hybrids,” Smith said. Rasmussen said he’s excited to be able to make those distinctions in Upper Klamath Lake.

Having that extra assurance beyond physical identification will also be crucial for sucker recovery efforts, which harvest larvae from the wild to raise in captivity and eventually release. Those genetic markers will help biologists ensure they’re saving the right species.

There’s still a chance the fully completed analysis could find genetic differences in the Lost River populations, but Rasmussen said their absence doesn’t necessarily mean shortnose and largescale suckers there aren’t still separate species. Given the mind-bogglingly interwoven history of suckers in the Basin, hybridization is a common evolutionary process that can in some cases promote the survival of populations. Plus, morphological and behavioral differences between the fish still remain.

“At an early level, we’re taught, ‘Species are species and that’s that,’” Rasmussen said. “That’s not really how things work. Things are much more nuanced in real life.”

Though scientists have yet to find a way to genetically distinguish shortnose and largescale suckers in the Lost River, they can still rely on non-genetic signals in a management context. The Service drafted a policy regarding species hybridization several decades ago before genomics research really took off, and though it was never officially enacted, it directed managers to base their decisions off of non-genetic factors: If it looks and behaves enough like an ESA-listed species, a hybrid can still be protected.

As of now, Rasmussen said yet another study confirming the lack of a genetic difference between shortnose and largescale suckers in the Lost River Basin won’t have an immediate effect on management practices there, particularly as it pertains to ESA implementation. But he said the Service plans to gather experts and Smith’s research team together to determine if their findings warrant any long-term changes in conservation practices.

“Having a better understanding of what the patterns are out there gives us the ability to actually make some more specific plans,” he said. “Once we get some clarity there, we’ll include it in our decision-making process.”

Rasmussen said it’s important to embrace the gray area. That approach is reflected in the traditional ecological knowledge of the Klamath Tribes, who have multiple linguistic distinctions for the Basin’s fish depending on their physical characteristics—certainly more than the four species today’s scientists have landed on. Rasmussen recalls a conversation with a tribal elder who remembers specific times and places one could catch Yen versus Koptu, and he thinks those teachings likely came from observing the complex interplay between hybridization and speciation over thousands of years.

“As humans, we like to look at [species] and we like to say, ‘This one belongs to this box, and this one belongs to this box,’ and evolution doesn’t do that,” Rasmussen said. “Sometimes they bleed into each other, and it’s hard to tell where things stop.”

Josh Rasmussen, Klamath sucker program coordinator for the U.S. Fish and Wildlife Service, said that geographic and temporal separation is what divides the Basin’s sucker population into separate species. If they don’t spawn at the same time, there’s little chance of them mixing genetic material and giving rise to offspring with physical and behavioral characteristics of multiple species. But as the fish’s habitats have changed, Rasmussen said, hybridization has become more common in recent years.

“As you have this back and forth of isolation, it kind of makes the picture a little difficult to really tease out,” he said.

Previous research has found that recent droughts and water management actions in the Basin have pushed the two Catostomus species and the lake suckers closer together. C’waam and Koptu typically head into the rivers to spawn during April and May, roughly a month later than their river-dwelling cousins.

Other lake suckers in the Great Basin have hybridized in response to human activity, like the June and Utah suckers, which began spawning together after settlers altered the hydrology of Utah Lake. It only takes a few individuals overlapping their spawning with another species to produce hybrid offspring.

“It doesn’t have to be the whole population spawning on top of each other,” Rasmussen said. “It could just be a couple of weirdos.”

Many decades of spawning by those weirdos have turned the Klamath Basin’s genetic landscape of suckers into a tangled mess. Matt Smith, a fish biologist at the U.S. Fish and Wildlife Service’s Abernathy Fish Technology Center in southwest Washington, is working on the latest effort to unravel it.

Presented at the Service-hosted Sucker Symposium earlier this month, Smith’s research used the latest genomic technology to determine where in the Basin the four species overlapped genetically. Though a full data analysis has yet to be completed, Smith said his findings so far support previous studies that found no detectable genetic difference between shortnose and largescale suckers in the Lost River Basin.

That’s despite often-clear differences between the two species’ morphology and habitat. For example, largescale suckers, adapted to riverbed feeding, tend to have fleshier lips than shortnose suckers, who have adapted to feeding on algae and invertebrates in lakebeds.

Smith and his colleagues, including researchers at a genetics lab at the University of California Davis, used a relatively new technology called restriction site associated DNA (RAD) sequencing to analyze the genomes of about 700 fish, samples from whom had been taken over the past three decades.

Instead of using significant energy and time to scan a fish’s entire genome, the RAD technique compiles representative fragments that are easier for a computer to digest. Researchers aligned these fragments to reconstruct an abbreviated genome for each species and sequenced individual samples against it.

Sucker samples were taken from the Upper Klamath Lake watershed, the Upper Williamson River, the Klamath River below Lake Ewauna and the Lost River Basin. Smallscale suckers, which are the only species not endemic to the Klamath Basin, also had some samples taken from the Rogue River. Smith said part of the study’s purpose was to identify genetic markers that researchers could use to cross reference species in the field, allowing them to be more sure about which species of sucker they collect.

“Our results were the same as previous genetic work in that it’s fairly easy to differentiate Lost River and shortnose, but it was still a little bit complicated for shortnose and largescale,” Smith said.

That difference wasn’t evident on a genetic level for the two species in the Lost River Basin. However, unlike previous research, the study was able to find genetic markers that could differentiate between them in the Upper Klamath Lake drainage basin. Smith said that could be helpful to field researchers identifying specimens in that area.

“This research looks promising for the ability to not only differentiate those two species but also identify hybrids,” Smith said. Rasmussen said he’s excited to be able to make those distinctions in Upper Klamath Lake.

Having that extra assurance beyond physical identification will also be crucial for sucker recovery efforts, which harvest larvae from the wild to raise in captivity and eventually release. Those genetic markers will help biologists ensure they’re saving the right species.

There’s still a chance the fully completed analysis could find genetic differences in the Lost River populations, but Rasmussen said their absence doesn’t necessarily mean shortnose and largescale suckers there aren’t still separate species. Given the mind-bogglingly interwoven history of suckers in the Basin, hybridization is a common evolutionary process that can in some cases promote the survival of populations. Plus, morphological and behavioral differences between the fish still remain.

“At an early level, we’re taught, ‘Species are species and that’s that,’” Rasmussen said. “That’s not really how things work. Things are much more nuanced in real life.”

Though scientists have yet to find a way to genetically distinguish shortnose and largescale suckers in the Lost River, they can still rely on non-genetic signals in a management context. The Service drafted a policy regarding species hybridization several decades ago before genomics research really took off, and though it was never officially enacted, it directed managers to base their decisions off of non-genetic factors: If it looks and behaves enough like an ESA-listed species, a hybrid can still be protected.

As of now, Rasmussen said yet another study confirming the lack of a genetic difference between shortnose and largescale suckers in the Lost River Basin won’t have an immediate effect on management practices there, particularly as it pertains to ESA implementation. But he said the Service plans to gather experts and Smith’s research team together to determine if their findings warrant any long-term changes in conservation practices.

“Having a better understanding of what the patterns are out there gives us the ability to actually make some more specific plans,” he said. “Once we get some clarity there, we’ll include it in our decision-making process.”

Rasmussen said it’s important to embrace the gray area. That approach is reflected in the traditional ecological knowledge of the Klamath Tribes, who have multiple linguistic distinctions for the Basin’s fish depending on their physical characteristics—certainly more than the four species today’s scientists have landed on. Rasmussen recalls a conversation with a tribal elder who remembers specific times and places one could catch Yen versus Koptu, and he thinks those teachings likely came from observing the complex interplay between hybridization and speciation over thousands of years.

“As humans, we like to look at [species] and we like to say, ‘This one belongs to this box, and this one belongs to this box,’ and evolution doesn’t do that,” Rasmussen said. “Sometimes they bleed into each other, and it’s hard to tell where things stop.”