Biological Opinions - Bureau of Reclamation

12.2.6.2 Marine Derived Nutrients
Marine-derived nutrients are nutrients that are accumulated in the biomass of salmonids while
they are in the ocean and are then transferred to their freshwater spawning sites where the salmon
die. The return of salmonids to rivers makes a significant contribution to the flora and fauna of
both terrestrial and riverine ecosystems (Gresh et al. 2000), and has been shown to be vital for
the growth of juvenile salmonids (Bilby et al. 1996, 1998, Giannico and Hinch 2007, Wipfli et
al. 2003, 2004, 2010). Evidence of the role of marine-derived nutrients and energy in
ecosystems suggests this deficit is likely to result in an ecosystem failure contributing to the
downward spiral of salmonid abundance (Bilby et al. 1996). Reduction of marine-derived
nutrients to watersheds is a consequence of the past century of decline in salmon abundance
(Gresh et al. 2000).
12.2.6.3 Artificial Propagation
Three artificial propagation programs are considered to be part of the ESU: the Cole Rivers
Hatchery (Rogue River), Trinity River Hatchery, and Iron Gate Hatchery (IGH, Klamath River)
coho programs. These hatcheries produce not only coho salmon but also Chinook salmon and
steelhead for release into the wild. Iron Gate (IGH), Trinity River, and Cole Rivers hatcheries
release roughly 14,215,000 hatchery salmonids into SONCC coho salmon ESU rivers annually.
Annual coho salmon production goals at these hatcheries are 75,000, 500,000, and 200,000,
respectively. In addition to the three hatcheries, the Mad River and Rowdy Creek hatcheries in
California and the Elk River Hatchery in Oregon produce steelhead and Chinook salmon that can
prey on or compete with wild SONCC ESU coho salmon.
Natural populations in these basins are heavily influenced by hatcheries (Weitkamp et al. 1995;
Good et al. 2005) through genetic and ecological interactions. Genetic risks associated with outof-basin
and out-of-ESU stock transfers have largely been eliminated. However, two significant
genetic concerns remain: 1) the potential for domestication selection in hatchery populations
such as the Trinity River, where there is little or no infusion of wild genes, and 2) straying by
large numbers of hatchery coho salmon either in basin or out-of-basin. Spawning by hatchery
salmonids in rivers and streams is often not controlled (Independent Scientific Advisory Board
2002) and hatchery fish stray into rivers and streams, transferring genes from hatchery
populations into naturally spawning populations (Pearse et al. 2007). CDFG (2002b) found that
29 percent of coho salmon carcasses recovered at the Shasta River fish counting facility had left
maxillary clips in 2001, indicating that they were progeny from the IGH. The average
percentage of hatchery coho salmon carcasses recovered at the Shasta River fish counting facility
from 2001, 2003, and 2004 was 16 percent (Ackerman and Cramer 2006). Although the actual
percentages of hatchery fish in the river change from year to year and depend largely on natural
returns, these data indicate that straying of IGH fish do occur in important tributaries of the
Klamath River.
The transferring of genes from hatchery fish can be problematic because hatchery programs have
the potential to significantly alter the genetic composition (Reisenbichler and Rubin 1999, Ford
2002), phenotypic traits (Hard et al. 2000; Kostow 2004), and behavior (Berejikian et al. 1996)
of reared fish. Genetic interactions between hatchery and naturally produced stocks can decrease
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