The number of cats in an area should be pretty closely related to the number of people living in the area. The more cats, the more people, and it would not be hard to believe that having more people in an area might lead to more environmental destruction and displaced habitats.
The control featured in the paper is Europe, where the domestic cat is younger and not as well adapted, environmentally, as that in America. There is significantly less environmental destruction, despite the controls featuring similar numbers of the animals. Simply having cities has not had a similar effect.
