The Uneasy Chair has an interesting Earth Day post that quotes extensively from a newspaper article about the bay checkerspot butterfly, noting its near extinction though it had "the protection of the Endangered Species Act, a 443-page recovery plan and 45 years of intense scientific study."

The bay checkerspot's downfall started more than 200 years ago when Europeans arrived in California. They brought grasses such as rye and wheat, which soon blanketed the landscape and squeezed out native plants that the checkerspots relied on. . .

In 1960, a decade before the first Earth Day, Stanford University biologist Paul Ehrlich began tagging and counting bay checkerspots at the university's Jasper Ridge Biological Preserve.

The butterfly became one of the most studied wild animals in the world -- a sort of lab rat for understanding how populations of animals function, flourish and decline.

Over the years, the scientists closed Jasper Ridge to the public and removed grazing cattle. Yet in spite of all their efforts, by 1997 the preserve's butterflies were gone.

It turns out that removing the cattle may have been a mistake. Cows like to eat European grasses, but leave native plants alone, so their grazing actually helped keep the habitat healthy. . .

Researchers also worry about a more subtle killer: fertilizer, in the form of ammonia and other nitrogen compounds that billow from smokestacks and tailpipes and settle onto the ground. Add enough fertilizer to serpentine soil, and it suddenly becomes a good place for European grasses to grow.

See Fat and Happy for more information about the effects of nitrogen and grazing on swards. Any grazier could, and probably did, predict the consequnces for sward diversity when grazers are excluded. I expect fire was prevented too. You get what you manage for whether you realize what that is going to be or not. The scientists managed for invasive cool season Eurasian annual grasses such as rye. They just didn't know anything about grass and so didn't realize what they were doing. Typical, and hard on butterflies.