SIOUX FALLS (AP) - The Topeka shiner was doing relatively well in the creeks and rivers where it lives in eastern South Dakota, so the U.S. Fish and Wildlife Service in 2005 decided not to include the state's waters as designated critical habitat for the minnow it had listed as endangered in 1998.
South Dakota's management plan for the fish, with its goal of maintaining existing stream habitat as the best way to achieve the recovery and future delisting of the shiner, also was persuasive in the service's decision. The plan was developed by the departments of Game, Fish and Parks and Agriculture.
In the years since the U.S. Fish and Wildlife Service decision, though, land use in the proposed critical habitat of the Big Sioux, Vermillion and James River drainages has undergone notable change. Conservation Reserve Program grassland is being returned to row crop production, and the use of tile drainage has been stepped up to improve yields on farm land.
"We know the land is changing quickly," said Rob Klumb, project leader and fisheries biologist for the USFWS Great Plains Conservation Office.
Are those changes adversely affecting Topeka shiner stream habitat?
"We don't know, but we're going to try to find out," Klumb said.
"It's a legitimate issue. That's why we want to do some of this work."
He hopes to secure grant funding for a new study of the shiner in South Dakota, perhaps as soon as 2013
When researchers take to the field, they might have a powerful new research tool. Klumb hopes to use environmental DNA analysis in stream surveys to determine the presence of Topeka shiners.
The process was developed by University of Notre Dame biologist David Lodge, who is using it to look for Asian carp in the Great Lakes. It rests on the theory that because everything sheds DNA over its lifetime, a water sample can be analyzed for DNA to determine whether a species exists upstream of where the sample was taken.
"A lot of people are turning to this as a viable technique now. It hasn't been around long enough to be really, truly vetted. But it's getting there," said Matt Powell, the associate director of the University of Idaho Aquaculture Research Institute. Almost a decade ago, Powell reviewed a National Science Foundation research proposal that involved one of the first uses of environmental DNA analysis.
"It totally blew me away," he said. "It's a really novel method, and it has potential to be very transformative in the way we look at communities."
Enormous increases in computer capability makes it possible.
"We're not talking gigabytes," 1 billion units of information. "We're talking terabytes," 1 trillion units, Powell said.
Finding and sequencing DNA "is relatively straightforward," he said. "The number of DNA sequences we can get out of a sample is tremendous. Teasing out the sequence you're looking for requires high expertise and a lot of computing power.
"The amount of data is not the linchpin. The linchpin is being able to manipulate it and make sense of it."
While Topeka shiner populations might be influenced by increased nitrate levels in water as a result of tile drainage, there is great momentum for increasing its use. Record income for farmers the past two years both encourages them to pursue higher crop