**External Independent Peer Review by the Center for Independent
Experts**

**Assessment of NMFS' Draft Biological Opinion on the**

**Bureau of Reclamation's Klamath Project Operation**

**Project Background:**

The purpose of this independent review is to evaluate and comment on the
use of the best available scientific and commercial information in our
draft biological opinion concerning effects of the Bureau of
Reclamation's (Reclamation's) Klamath Project Operations (Project) on
the listed threatened Southern Oregon/Northern California Coast (SONCC)
coho salmon (*Oncorhynchus kisutch*) and its designated critical habitat
for the period of 2008 through 2018. The review will focus on the
technical aspects of the NMFS draft biological opinion; the review will
not determine if NMFS' conclusions regarding the project's potential to
adversely modify or destroy critical habitat or jeopardize the continued
existence or recovery of listed SONCC coho salmon are correct.

Due to water limitations to meet all of the needs of humans, wildlife
and fisheries resources, NMFS' 2001 and 2002 biological opinions on the
effects of the Bureau of Reclamation's Klamath Project Operation
(Project), including water deliveries to the Klamath Irrigation Project,
have been subject to intense scrutiny and litigation. In an effort to
ensure we correctly analyzed the effects of the Project, NMFS sought
review from the National Academies Committee on Endangered and
Threatened Fishes in the Klamath River Basin (NRC) on the strength of
scientific support for the biological assessment and biological opinion.
The NRC released its 2002 Interim Report on NMFS' 2001 biological
opinion and their conclusions included:

-   A lack of evidence indicating high mainstem flows influence coho
    year class strength.

-   The relative increase in available habitat for coho salmon in the
    mainstem Klamath River resulting from higher flows required in NMFS'
    Reasonable and Prudent Alternative to the Proposed Action were
    minor.

-   A lack of scientific evidence in the Klamath River of a positive
    relationship between mainstem Klamath River flows and coho smolt
    survivorship.

-   Higher summer flows could be disadvantageous by further increasing
    water temperature and reducing available thermal refugial habitat in
    the mainstem Klamath River.

Following the release of NMFS' 2002 biological opinion on the Project
for the period 2002-2012, the NRC released their Final Report on
Endangered and Threatened Fishes in the Klamath River Basin (2004) in
which the above conclusions were reiterated and additional information
and recommendations for the continued survival of Klamath River coho
salmon were provided.

Coincident to the NRC's review and recommendations, NMFS sought peer
review on its Central Valley Project and State Water Project Operations,
Criteria, and Plan (OCAP) biological opinion. NMFS asked the CalFed
Bay--Delta Authority Science Program (CBDA) and the Center for
Independent Experts (CIE) each to conduct independent peer reviews to
evaluate whether the scientific information used in the biological
opinion was the best available. The peer review reports raised multiple
and complex issues that merited evaluation in the context of future
improvements to NMFS' biological opinions on large-scale projects
(*i.e*., OCAP, Klamath Project Operations). In response to the OCAP
reviews, NMFS' Science Center developed recommendations and guidance for
the development of future NMFS biological opinions. NMFS' Science Center
Review (Lindley *et al.* 2006) includes recommendations to improve the
conceptual framework of section 7 analyses on large-scale projects. NMFS
has in hand a general life cycle approach outlined by the Viable
Salmonid Populations (VSP) report (McElhaney *et al*. 2000). VSP is
accepted by NMFS as best available science. Lindley *et al.* (2006)
concluded that within the framework provided by VSP, further
improvements could be made by systematically examining all of the
important linkages between project effects and VSP parameters,
addressing climate variation and climate change, accounting for
uncertainty, and making the connections between data, assumptions,
analyses, and conclusions more transparent.

[New Information]{.underline}:

NMFS' draft biological opinion will utilize the body of new scientific
information on coho salmon in the Klamath River. This information
includes (1) SONCC Technical Recovery Team documents defining the
historical population structure of Klamath River basin coho salmon
(Williams *et al*. 2006), and population viability (Williams *et al*.
2007); (2) Cramer Fish Sciences Klamath River Coho Life Cycle Model; (3)
Evaluation of Instream Flow Needs in the Lower Klamath River Phase II
Final Report (Hardy *et al*. 2006) ; (4) Reclamation's Undepleted
Natural Flow Study Final Report (Reclamation 2005); (5) NRC's Review of
Hardy et al. 2006, and Reclamation 2005; (6) new information on the
effects of mainstrem flow and water quality on fish disease; and (7)
other information provided in Reclamation's final biological assessment
(2007). The breadth of new information includes disparate conclusions
relevant to the potential effects of the Project on coho salmon and NMFS
will need to reconcile these disparate conclusions in our draft
biological opinion.

**Terms of Reference**

CIE reviewers shall evaluate the draft Opinion to determine whether the
following questions resulting from the Science Center review are
adequately addressed:

1.  Does the draft biological opinion incorporate an ecological
    framework that emphasizes the geographic structure of habitats,
    populations, and diverse salmon life histories that contribute to
    salmon resilience and productivity (*i.e*., VSP concept, see
    McElhaney *et al*. 2000 and Lindley *et al*. 2006)?

2.  Does the draft biological opinion consider a range of climatological
    conditions and water demand scenarios in the analysis?

3.  Does the draft biological opinion consider a range of ocean
    conditions in the analysis?

4.  Does the draft biological opinion consider the effects of hatchery
    fish on listed fish?

Additionally, CIE reviewers shall evaluate the draft biological opinion
to determine whether the following questions resulting from the NRC's
2002 and 2004 reports are adequately addressed:

5.  Did NMFS' draft biological opinion present convincing scientific
    evidence about the spatial and temporal extent of young-of-year and
    juvenile coho salmon use and occurrence in the mainstem Klamath
    River?

6.  Has the draft biological opinion adequately evaluated the potential
    effects of mainstem flows on the survivorship of coho smolts?

7.  Are the draft biological opinion's scientific findings on the
    influence of mainstem flows on the spatial and temporal extent of
    coho juvenile survivorship in the summer months scientifically
    supportable?