You may well remember the controversy of the 1980s and 1990s over the apparently-declining numbers of Northern Spotted Owls in the Pacific Northwest. The Spotted Owl (Strix occidentalis) population of the Western United States is actually made up of three, closely-related subspecies, the Northern Spotted Owl (Strix occidentalis caurina), the California Spotted Owl (Strix occidentalis occidentalis) and the Mexican Spotted Owl (Strix occidentalis lucida).
This source provides some information about the range and habitats of the Spotted Owls, as well as the recently-recognized competition from its close relative, the larger Barred Owl (Strix varia).
From the Answers.com link (with slight paraphrasing):
...The nearly contiguous range of the Northern Spotted Owl extends from SW British Columbia south through western Washington and Oregon through the north-central coast of California.
The range of the California Spotted Owl overlaps the range of the Northern Spotted Owl in the southern Cascade Mountain Range, and extends south through the western Sierra Nevada to Tulare County, CA. Discrete populations of the California Spotted Owl also occur in mountainous areas of coastal and southern California from Monterey County to northern Baja California.
In the United States the Mexican Spotted Owl occurs in geographically separated populations in mountain ranges and canyons of Utah, Colorado, Arizona, New Mexico, and extreme western Texas. In Mexico it ranges from Sonora, Chihuahua, Nuevo León, and eastern Coahuila through the Sierra Madre Occidental and Sierra Madre Oriental as far south as Michoacán...
For the original citations and more information, please see the Answers.com entry.
Within the realm of nature, it is not unusual for there to be more than one reason for something happening. Habitat-loss due to logging and other events, e.g., the Mount St. Helens eruptions and windstorms, has been cited as a significant cause of population declines. More recently, the apparent entry of the larger Barred Owl into the ranges of the California and Northern Spotted Owls has resulted in population declines due to the Barred Owls being: 1) More aggressive in territorial defense; 2) Having a broader (more adaptable) diet and; 3) Occurring in more varied habitats. As the Barred Owls are closely-related (having had a common ancestor in the recent past), there is some hybridization in the overlapping areas, blurring the distinction between the Barred Owl and the Spotted Owl.
So, there appears to be a combination of human influences and natural influences in the changes facing the Spotted Owls. Unfortunately (from the title-linked article), some people in the Federal Government are of the opinion that these changes need to be "stopped" by intervening and killing at least some of the Barred Owls in the range of the Northern Spotted Owls. Rather than letting "nature take its course."
As both species occupy the same niche in their habitat overlaps - thus there are niche overlaps and habitat overlaps - under entirely-natural conditions, the Barred Owl would eventually dominate the Spotted Owls, forcing the Spotted Owls to: 1) Migrate to find other habitats with less competition; 2) Engage in Resource Partitioning (finding other food sources in the same habitat) or; 3) Become extinct. It is not "fair", but it is "nature's way."
These Secondary/Tertiary Carnivores serve to keep predated species population numbers under control and though part of this issue may be due to human intervention, humans "playing favorites" among the predators may lead to "unintended consequences". It might be better for the humans to resist their temptation to "make things more fair" and just sit back, watch, and learn from this event, as it unfolds.