Biological Opinions - Bureau of Reclamation

(200,000) are much smaller in number and although there are likely to be some adverse
competitive interactions that occur between these groups, other factors related to disease and the
poor condition of habitats in the major tributary streams likely have a greater impact on survival
of wild coho salmon. Modeling conducted for CDFW’s IGH HGMP indicates that the release
of 75,000 coho salmon juveniles has the potential to reduce natural coho salmon juvenile
abundance by up to 6 percent through increased predation, competition and disease, assuming
the natural juvenile coho salmon abundance is 75,000 (CDFG 2012). The impact is lower if
natural population abundance is greater than 75,000 and higher if the natural abundance is lower
than 75,000 (CDFG 2012).
A Draft HGMP has been developed for IGH as part of the CDFW’s application for an ESA
section 11(a)(1)(A) permit for hatchery operation (CDFG 2012; 78 FR 1200, January 8, 2012; 78
FR 6298, January 30, 2013). The HGMP is intended to guide hatchery practices toward the
conservation and recovery of listed species, specifically, the upper Klamath River coho
population. Although the HGMP has yet to be approved, the CDFW began implementing in
2010 some of the recommended changes to the management of IGH coho salmon, including the
use of a genetic parental based spawning matrix to reduce potential inbreeding and improve
fitness over time (Chesney and Knechtle 2011c).
In a review of 270 references on ecological effects of hatchery salmonids on natural salmonids,
Flagg et al. (2000) found that, except in situations of low wild fish density, increasing release
numbers of hatchery fish can negatively affect naturally produced fish. Also evident from the
review is that competition of hatchery fish with naturally produced fish almost always has the
potential to displace wild fish from portions of their habitat (Flagg et al. 2000). The increase in
density of juvenile salmonids, combined with the reduction in instream habitat resulting from
decreased flows in June resulting from hydrologic alteration of the Klamath River (see
Hydrologic Alteration section above), are likely to have negative impacts on coho salmon
juveniles. During the summer, sometimes hundreds or even thousands of juvenile salmonids can
be forced by water temperatures into small areas with cold water influence (Sutton et al. 2007).
Another important consideration in regards to SONCC coho salmon ESU diversity, spatial
structure, and productivity is how smaller coho salmon populations from tributaries such as the
Scott and Shasta rivers, which are important components of the ESU viability, are affected by
straying of hatchery fish. The average annual percentage of hatchery coho salmon in the Shasta
River from 2001 to 2010 was 23, with a high of 73 in 2008 (Chesney and Knechtle 2011a,
Ackerman et al. 2006). These data indicate that a fair amount of straying of IGH fish occurs into
important tributaries of the Klamath River, like the Shasta River, which has the potential to
reduce the reproductive success of the natural population (Chilcote 2003, Mclean et al. 2003,
Araki et al. 2007, Chilcote et al. 2011) and negatively affect the diversity of the interior Klamath
populations via outbreeding depression (Reisenbichler and Rubin 1999, HSRG 2004). However,
recent preliminary findings by NMFS Southwest Fisheries Science Center suggest that hatchery
and wild fish have already interbred in the Klamath basin, and a pure wild stock no longer exists
(CDFG 2012). The total impacts of hatchery strays on Klamath River populations are not well
understood. However, known straying data and preliminary genetic typing indicate that hatchery
releases have negatively impacted wild populations, particularly in the upper basin.
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