EPA's Vessel General Permit and Small Vessel General

alter macroinvertebrate communities and habitats, affecting the forage base for salmon and trout
(McCarthy et al. 2009, Williams et al. 2009).
Fishing pressure has also negatively impacted salmon populations. Fishing reduces the number
of individuals within a population and can lead to uneven exploitation of certain populations and
size classes (Reisenbichler 1997). Targeted fishing of larger individuals results in excluding the
most fecund individuals from spawning (Reisenbichler 1997). Genetic changes that promote
smaller body sizes have occurred in heavily exploited populations in response to size-selective
harvest pressures (Reisenbichler 1997). Fishing pressure can reduce age at maturity in fished
populations as the fished populations compensate for the reductions in the numbers of spawning
adults (Reisenbichler 1997).
Each year hatcheries along the west coast of the United States release nearly 1.2 billion juvenile
salmon (Mahnken et al. 1998), with 200 million salmon released annually into the Columbia
River alone. Hatcheries have the potential to reduce the viability of natural salmon populations
through behavioral or reproductive incompatibility, introgression, and the alteration of run times
(Ruckelshaus et al. 2002). These potential risks are not trivial; in chinook populations where
hatchery fish are marked, escaped hatchery salmon can constitute up to 60% of the spawning
population in areas without planned supplementation programs (Ruckelshaus et al. 2002).
Aquatic nuisance species (ANS), also described as non-native or invasive species, adversely
affect listed salmon species through several mechanisms, including: predation, competition,
trophic structure alteration, introgression, and transfer of pathogens. ANS pose as great or
greater threat to the continued existence of salmonid species as the four Hs (Sanderson et al.
2009). Channel catfish, small and largemouth bass, and walleye prey on juvenile salmon
(Sanderson et al. 2009). Juvenile shad prey heavily on zooplankton, which are also the primary
prey for juvenile Chinook salmon (Haskell et al. 2006). The presence of brook trout in the
Columbia River Basin is associated with a 12% reduction in the survival of juvenile salmon
(Levin et al. 2002). Non-native crustaceans, mollusks, and plants pose significant risks to
salmonids and the function of their ecosystems. For example, the invasive New Zealand mud
snail has been detected in the diet of juvenile Columbia River Chinook salmon, indicating the
potential for a shift in estuarine food web structure (Bersine et al. 2008). Non-native quagga and
zebra mussel invasions in the eastern U.S. have resulted in competition with native mussels,
disruption of food webs, and bioaccumulation of toxins; similar threats are expected if these
species invade western waterways (Sanderson et al. 2009). Aquatic plants, such as purple
loosestrife and Eurasian water milfoil, have been introduced to the Pacific Northwest through
ballast water. These rapidly decomposing plants have the potential to alter ecosystem function
through changes in seasonal nutrient availability and depressed dissolved oxygen concentrations
(Unmuth et al. 2000, Blossey et al. 2001, Cronin et al. 2006). Climate change is likely to
facilitate the establishment and expansion of ANS. In summary, non-native species have
adversely affected salmonid species, primarily through predation and competition; however, they
also have the potential, through the mechanisms listed above, to equal or exceed the impacts
caused by overharvest, habitat loss, hatcheries, and threats to the hydrosystem (Ruckelshaus et
al. 2002, Sanderson et al. 2009).
Pacific salmon species are exposed to a number of contaminants throughout their range and life
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