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Nonetheless it seems that the idea of prairie dogs being wiped out in a fearsome campaign on of carno-murine bioweapon genocide has caused a heated debate in the world of subterranean dog-squirrel boffinry.
prairie dogs themselves are nasty, nasty creatures. They eat their own. Seriously, they will commonly scavenge amongst roadkilled peers, which is why you'll often see four or five corpses littered along the same spot of road. They eat their young and the young of their neighbours, particularly in crowded situations (which happens frequently because they reproduce exponentially), and as the article points out, they are a major vector for bubonic plague. Plus they are filthy, noisy creatures that make an unholy mess out of any unsupervised landscape. The problem with trying to "manage" them is that without adequate predation, the only way TO manage them is to ruthlessly trap and cull them. They breed just that quickly. And they are NOT CUTE.
Most of the prairie dog populations that you see around Boulder are products of heavily overcrowded communities that the local hippies are too hippy-dippy to relocate/eradicate/manage, so they're universally dirty, mangy, greasy, skinny, wretched-looking things. They're simply rats with a better PR agent.
The only purpose they serve ecologically is as prey for local raptors, black-footed ferrets, and also apparently for grasshopper mice.
Prairie dogs are adorable! My mom wouldn't let me have one as a kid because they are (were?) known to carry the bubonic plague. But they would hang out in our backyard and in the field across the nearest major road (now condos I think). I feel bad for the little guys.