For a total picture, I highly recommend reading the new book by investigative historian Mark Dowie titled "Conservation Refugees: The Hundred-Year Conflict Between Global Conservation and Native Peoples." Much of the book focuses on situations in the (so-called) Third World, but it necessarily begins with Yosemite, which in so many ways embodies classical American conservation efforts, which then spread around the world.
This is a *very* provocative book. John Muir emerges as a somewhat difficult figure -- godfather of American conservation, founder of the Sierra Club, influential writer and naturalist, and a guy who wanted all the Indians out of Yosemite even though they had occupied that part of the Sierra Nevada for more than 2,500 years. He complained about the "uncleanliness" of the Ahwahneechee tribe that occupied the valley and called them "debased fellow human beings." And he's not the only conservation leader who may have feet of clay.
Dowie, by the way, is not some shrill writer with an agenda. He's thoughtful and thorough. Earlier in his career he wrote the article that forced Ford to recall the Pinto due to exploding gas tanks.