With elections nearing, some say the move was politically motivated.
About 5,000 acres (2,000 hectares) of national grassland will be chemically treated, says Art Smith, wildlife damage management program administrator for South Dakota Game, Fish, and Parks. The federal government has hired the state agency to do the work.
Another 13,000 acres (5,200 hectares) of adjacent private land has already been treated, he said, and that work was funded by the state.
Smith estimates 230,000 acres (93,000 hectares) in the state are inhabited by prairie dogs, so the amount being killed is only a small fraction.
"Anybody who thinks prairie dogs are endangered seriously needs to come to southwestern South Dakota," he said.
Jonathan Proctor, Northern Plains program director for Predator Conservation Alliance in Denver, Colorado, believes the prairie dogs are being unfairly blamed for eating all the vegetation.
The real problem, he said, is the drought.
"The prairie dogs are the scapegoats, because it's easier to blame them than God," Proctor said.
In September eight wildlife protection groups, including Predator Conservation Alliance, sued the federal government to try to stop the poisoning.
A settlement was reached in early October, cutting 3,000 acres (1,200 hectares) from the original poisoning plan. The agreement also struck down a proposal that would have allowed the dogs to be shot.
Also, under the deal no more poisonings will take place until the government conducts an environmental-impact study, which conservationist hope will lead to permanent protections for prairie dogs and ferrets in the area.
"Those are some pretty big concessions we got," Proctor said. "We felt over the long run it will mean less wildlife deaths than otherwise would happen."
Many species depend on the prairie dog for food or habitat, such as the swift fox, burrowing owl, and ferruginous hawk.
But the animal that concerns conservationists the most is the black-footed ferret, a native species considered extinct until 1981, when a few survivors were found in Wyoming.
Shortly after the find, a captive breeding and reintroduction effort started. Of the nine sites where ferret reintroduction has been attempted, only Buffalo Gap National Grasslands is considered successful, mainly because of the large prairie dog population.
"I think of Conata Basin as the cradle of ferret recovery," said Travis Livieri of Prairie Wildlife Research in Wall, South Dakota.
The nonprofit group works closely with the U.S. Forest Service, which is in charge of managing the Conata Basin and its ferret population.
Last year 264 ferretsmore than half of the wild populationlived there, he said.
Steve Forrest, a biologist and senior program officer for the World Wildlife Fund in Bozeman, Montana, says the poisoning will have some impact on the ferrets, because they rely on the dog's burrows for shelter.
As prairie dog "towns" become spread out, it forces the ferrets to travel greater distances above ground, between burrows, he said. This makes them more prone to predators, like owls and coyotes.
Besides impacting ferrets, the poisoning won't stop the dogs from spreading onto adjacent private property, which is traditionally prairie dog habitat, Forrest said.
Maps from the 1960s show almost twice as many prairie dogs living in the area than today, he said.
"[Prairie dogs] seem to go back to old prairie dog towns," Forrest, said. "We've seen that time and time again when we poison them out because the burrow systems are already constructed underground. They have some ability to sense that."
Smith, who's overseeing the poisoning, doesn't believe the ferrets will suffer any negative repercussions.
What worries him is the backlash from landowners.
"Their desire is to get the (ferret) population removed off the landscape," Smith said. "They want it out."
With emotions running high on this issue, Smith hopes the argument will be kept in the legal arena and not result in "middle-of-the-night tactics" taken to kill the ferrets.
When the dust finally settles, Smith hopes the ferrets remain in the area.
"Losing a species is a heck of an immoral thing for humans to do," he said. "However, there's a certain requirement that when these species are put back into the environment that it doesn't overly impact something else." To appease landowners, a U.S. $80,000 grant from U.S. Fish and Wildlife was recently obtained by Prairie Wildlife Research, the organization involved with ferret recovery.
Livieri said the incentive money is for landowners who manage their property in a manner that maintains some health of prairie dog populations.
Other solutions conservationists have proposed to benefit both landowners and endangered species recovery efforts include land exchanges and vegetative buffers to stop the dogs from going onto private property.
Veteran rancher Charles Kruse, who owns 2,300 acres (930 hectares) next to the Conata Basin and leases federal land for his cattle to graze, says he wants financial reimbursement.
"I'm going to be losing well over a third of my income just this year alone," Kruse said. "If the people of this country want to run us over with prairie dogs then they can compensate us."
A few months ago Kruse said 650 acres (260 hectares) of his property was poisoned but that the dogs are already filling the area back up.
Kruse isn't the only one affected. All of the 20 landowners adjacent to the Conata Basin, he said, have been hurt in one way or another.
"This Endangered Species Act is one of the most dangerous things that we've got in our law books right now," he said. "When a rodent has more precedence than peoples' livelihoods all through this area, well, that's absolutely ridiculous."
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