Biological Opinions - Bureau of Reclamation

Pacific salmonids Oncorhynchus spp. substantially contributes to their persistence, and
conservation of such diversity is a critical element of recovery efforts (Beechie et al. 2006). The
findings of Waples et al. (2001) support the conclusion of Beechie et al. (2006) because they
found life history and genetic diversity showed a strong, positive correlation with the extent of
ecological diversity experienced by a species. The analysis by Williams et al. (2006) suggested
that substantial environmental variability (e.g. wet coastal areas and arid inland regions) within
the Klamath River Basin resulted in nine separate populations of coho salmon (see Status of the
Species). Because aquatic species have evolved life history strategies in direct response to
natural flow regimes (Taylor 1991; Waples et al. 2001; Beechie et al 2006), maintenance of
natural flow regime patterns is essential to the viability of populations of many riverine species
(Poff et al. 1997; Bunn and Arthington 2002).
Understanding the link between the adaptation of aquatic and riparian species to the flow regime
of a river is crucial for the effective management and restoration of running water ecosystems
(Beechie et al 2006), because humans have now altered the flow regimes of most rivers (Poff et
al. 1997; Bunn and Arthington 2002). When flow regimes are altered and simplified, the
diversity of life history strategies of coho salmon are likely to be reduced because life history and
genetic diversity have a strong, positive correlation with the extent of ecological diversity
experienced by a species (Waples et al. 2001). Any reductions in salmonid life history diversity
are likely to have implications for their persistence (Beechie et al. 2006).
11.1.3 Flow and Rearing Habitat Analysis
NMFS used the relationships of flow and habitat formulated by Hardy (2012) and Hardy et al.
(2006) to quantify how coho salmon fry and juvenile habitats vary with water discharge in the
mainstem Klamath River below IGD. The flow-habitat relationships provided by Hardy et al.
(2006) and Hardy (2012) represent the best available data on flow-habitat relationship in the
Klamath River. NMFS is not aware of any other studies that quantify the relationship between
discharge and habitat in the Klamath River mainstem.
Hardy et al. (2006) developed habitat suitability criteria for life history stages of anadromous
salmonids in the regulated mainstem Klamath River based on the fundamental concepts of the
ecological niche theory. The 2006 report defines an ecological niche as “the set of
environmental conditions (e.g., temperature, depth, velocity) and resources (things that are
consumed such as food) that are required by a species to exist and persist in a given location.”
Species and life stage specific habitat suitability criteria used in instream flow determinations are
an attempt to measure the important niche dimensions of a particular species and life stage (Gore
and Nestler 1988). These criteria are then used to measure niche changes relative to changes in
flow.
Empirical data on juvenile coho salmon in the mainstem Klamath River are limited. While
juvenile outmigration monitoring (e.g., downstream migrant traps) provides information on
distribution and emigration timing on the mainstem Klamath River, there are few observations of
juvenile coho salmon utilizing micro-habitat. Consequently, Hardy et al. (2006) developed
literature-based habitat suitability criteria to quantify habitat availability for juvenile coho
salmon within the mainstem Klamath River. Habitat suitability criteria were validated using the
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