Over the last 150 years, large stretches of salmon habitat have been eliminated by human activity: mining, livestock grazing, timber harvesting, and agriculture as well as recreational and urban development. The numerical effect is obvious: there are fewer salmon in degraded regions than in pristine ones; however, habitat loss also has the potential to reduce genetic diversity. This is most evident in cases where it results in the extinction of entire salmon populations. Indeed, most analysts believe that some kind of environmental degradation underlies the demise of many extinct salmon populations. Although some rivers have been recolonized, the unique genes of the original populations have been lost.

Large-scale disturbances in one locale also have the potential to alter the genetic structure of populations in neighboring areas, even if those areas have pristine habitats. Why? Although the homing instinct of salmon to their natal stream is strong, a fraction of the fish returning from the sea (rarely more than 15 percent) stray and spawn in nearby streams. Low levels of straying are crucial, since the process provides a source of novel genes and a mechanism by which a location can be repopulates should the fish there disappear. Yet high rates of straying can be problematic because misdirected fish may interbreed with the existing stock to such a degree that any local adaptations that are present become diluted. Straying rates remain relatively low when environmental conditions are stable, but can increase dramatically when streams suffer severe disturbance. The 1980 volcanic eruption of Mount Saint Helens, for example, sent mud and debris into several tributaries of the Columbia River. For the next couple of years, steelhead trout (a species included among the salmon ) returning from the sea to spawn were forced to find alternative streams. As a consequence, their rates of straying, initially 16 percent, rose to more than 40 percent overall.

Although no one has quantified changes in the rate of straying as a result of the disturbances caused by humans, there is no reason to suspect that the effect would be qualitatively different than what was seen in the aftermath of the Mount Saint Helens eruption. Such a dramatic increase in straying from damaged areas to more pristine streams results in substantial gene flow, which can in turn lower the overall fitness of subsequent generations.