Kevin Kingsland, a doctoral student in zoology, examines a tiny shovelnose sturgeon

Getting a closer view -- Kevin Kingsland, a doctoral student in zoology, examines a tiny shovelnose sturgeon while doing DNA identification work in the laboratory of Ed Heist, associate director of the Center for Fisheries, Aquaculture and Aquatic Science at Southern Illinois University Carbondale. Heist and his students are working on a U.S. Army Corps of Engineers conservation program for endangered pallid sturgeon, a close relative of the pictured shovelnose. (Photo by Russell Bailey)

March 03, 2015

Genetic research looks to save pallid sturgeon

by Tim Crosby

CARBONDALE, Ill. -- He refers to it as such, but the hunt that a researcher at Southern Illinois University Carbondale is helping conduct is far more difficult than finding the proverbial “needle in a haystack.” 

And yet, he helped not only find one, but two. 

Ed Heist, associate director of the Center for Fisheries, Aquaculture and Aquatic Science at SIU, directed research that recently genetically identified two larval pallid sturgeon that were caught in the lower Missouri River near St. Louis. Finding the tiny specimens, which are only about a half-inch long, is part of far-reaching research effort by conservation agencies and the U.S. Army Corps of Engineers to rescue the pre-historic fish from extinction. 

Heist and his laboratory examined tissue from the two larval pallid sturgeon, which were discovered as part of a sampling effort by the Missouri Department of Conservation. Pallid sturgeon is an endangered fish species native to the Missouri and Mississippi rivers.  Heist is part of the Missouri River Recovery Program, a collaborative, comprehensive effort led by the Corps in partnership with multiple agencies. 

The discovery will help agencies that are focused on saving the fish better target their work this year, while a research method developed by one of Heist’s students will help SIU greatly increase the number of genetic samples it can process this year. 

The fish’s ancestors appear in the fossil record dating back to around the time of dinosaurs. Its presence in North American rivers and around the world has made a great impact on human culture. It is also prized for its eggs – caviar – to the point of being overfished in most of the world. 

Heist, who has been working on the sturgeon issue for about 10 years, said research indicates a “bottleneck” in the fish’s lifecycle is occurring early in life, somewhere between the time it is spawned by its parents and the time it develops into a small, finger-length fish called a fingerling. 

A theory held by many researchers, and supported by an official “jeopardy opinion” from the U.S. Fish and Wildlife Service, points the blame at the many modifications made to the Missouri and Mississippi rivers during the last 80 years or so aimed at flood control and making them move navigable. In doing so, researchers believe, the Corps of Engineers also inadvertently destroyed habitat and spawning areas the fish needed to survive. 

“Pallid sturgeon have always been rare but we’ve noticed they’ve been in further decline in recent years,” Heist said. “During the 1930s and up through the 1960s, many dams and other structures were constructed on the Missouri River, for hydroelectric, flood control and navigation. The sturgeon were adapted to a free-flowing river, and this really interrupted that.” 

In particular, the fish for centuries was adapted to the annual spring pulse of water, which was released downstream as snows melted in mountains around the river. The river also would typically drop its level during the summer. The corps, with its mission to control flooding and maintain navigability of the river, combated these natural occurrences. 

The U.S. Fish and Wildlife opinion agreed that the way in which the corps was managing the river was in fact detrimental to the pallid sturgeon, placing the onus on that agency to come up with a plan to reverse that problem. 

One way in which the agency has attacked the problem is by breeding pallid sturgeon in captivity and stocking the river with young fish. The Corps did this at least twice during the 1990s and more extensively since then, and young fish stocked at that time are finally reaching sexual maturity. Researchers can tell from fish they tagged with transmitters and follow with high-tech sonar gear that the mature fish appear to be going through spawning activity. 

“We’re not sure why, but we’re just not seeing a lot of young pallid sturgeon resulting from this activity.” Heist said. “However, if you stock fingerlings they will mature. So there’s some sort of break in the life cycle between those two stages.” 

That’s where the current research is focused. 

When the parents spawn, pallid sturgeon eggs sink to the bottom for a few days before they hatch and begin drifting in the water column. They may drift for days or even weeks before the larva settles down to the bottom and starts feeding. 

Researchers have been busily searching for young pallid sturgeon that last couple years, using extremely fine plankton netting to seine the water for specimens. Their goal is to find some that are surviving during the “bottleneck” period, and then examine their habitat, stomach contents and other factors that may be contributing to their survival. 

One challenge they face, however, is the pallid’s cousin, the shovelnose sturgeon, which is more numerous, looks extremely similar to the pallid at maturity and is visibly indistinguishable as a larva or tiny fish. Add to that the fact the two fish sometimes interbreed, resulting in hybrid specimens. 

The only way to tell them apart is genetically, and Heist’s lab is focused in part on that task. Genetically identifying the first two lower Missouri River larval pallids, found last summer near St. Louis, will help researchers focus their efforts there and upstream during the coming spawning season, hopefully resulting in more success. 

“What we don’t entirely understand about pallid sturgeon is what kind of habitat they need -- what do they eat, what kind of habitat do they need to live and reproduce? So we need more biological data,” said Heist, who has worked on this effort for about five years. “We’ve screened thousands of larvae here at SIU, and these are the only two we’ve found so far from the lower Missouri River. But with these two, we know exactly, down to precise GPS coordinates, where they were caught. We know the habitat there. We only used their tails for DNA analysis while the Army Corps is doing further analysis of stomach contents and lipid analysis to try and identify what they like to eat.” 

Further analysis of stable isotopes in the specimens may also tell researchers where exactly in the river that their parents’ spawned, as isotope ratios vary along the river in a known fashion. 

“So there’s a lot more information to be gained from these two larvae, now that we know who they are.” 

And here’s a bonus mind-blower: Heist’s genetic analysis not only revealed the two larvae were pallid sturgeon, but siblings from the same spawn. 

Heist’s genetic research also helps the stocking program be more successful by reducing potential inbreeding that might occur in the wild among fish stocked from the upper Missouri River. That population, which is very old and genetically distinct from the lower Missouri River population, has not successfully reproduced in the wild in 50 years, Heist said.  

Many of the mature pallid sturgeon in the lower Missouri River were stocked from the genetically distinct upper Missouri River population. Heist’s DNA analysis of the two larvae showed they were not stocked from the upper Missouri River, but appear to have been wild fish. 

Doing all this DNA work, however, had been a slow and expensive process. That is until a doctoral student in Heist’s laboratory came up with a way to greatly speed things up. 

Jennifer S. Eichelberger, a doctoral student in zoology, developed a method to rapidly screen large numbers of larvae for possible pallid sturgeon, thus enabling the laboratory to screen many more potential finds. The old process involved a great deal of human interpretation and was very hands-on in that sense, Heist said. Eichelberger found a way to make the initial DNA marker screening process heavily automated, saving the more costly human hours for only good leads. 

“In the past, we could afford to do a few hundred a year, but this year we will do a few thousand for the same cost,” Heist said. “The Army Corps wants us to do 5,000 for them. When only about one in 1,000 samples is a pallid sturgeon – the needle in the haystack – this will have a big impact on how the research is conducted.” 

Once researchers unlock the secret to what is causing the decline in pallid sturgeon, the Army Corps of Engineers will make the needed adjustments, Heist said. 

“They love to build things and they are good at it,” he said. “They just need to know what to build, and we’re trying to find out.” 

Saving the pallid sturgeon and its cousins is an important front in the battle to save endangered species, Heist said. 

“Sturgeon are about the most imperiled fish on Earth,” he said. “There are about 30 species and just about all of them are in deep trouble. There are a lot of cultural ties to humans and they are very unique. That alone gives them a very high conservation value, and we would hate to lose them.”