Appendix B. Computational approach used in redundancy analysis (RDA) and variance partitioning.

Computational approach used in redundancy analysis (RDA) and variance partitioning

Appendix D. Summary of fish community metrics for each permanent sample site in Martis Creek, California, 1979–2008.

Summary of fish community metrics for each permanent sample site in Martis Creek, California, 1979–2008

Appendix A. Characteristics of the four permanent sample sites (S1-S4) in Martis Creek, California, 1979–2008.

Characteristics of the four permanent sample sites (S1-S4) in Martis Creek, California, 1979–2008

Appendix A. Tables showing fish species introduced into California watersheds.

Tables showing fish species introduced into California watersheds

Appendix A. Results of the indicators of hydrologic alteration (IHA) analysis for lower Putah Creek, California (USA).

Results of the indicators of hydrologic alteration (IHA) analysis for lower Putah Creek, California (USA)

Preferred and alternate linear mixed-effects models of factors influencing survival of Salmon River spring Chinook salmon, Salmon River fall Chinook salmon, Salmon River summer steelhead trout, and Scott River fall Chinook salmon, 1980–2007.

<p>Preferred and alternate linear mixed-effects models of factors influencing survival of Salmon River spring Chinook salmon, Salmon River fall Chinook salmon, Salmon River summer steelhead trout, and Scott River fall Chinook salmon, 1980–2007.</p

Name, explanation, source and transformation of variables used in modeling of salmonid survival from the Klamath River, California, USA, 1980–2012.

<p>Name, explanation, source and transformation of variables used in modeling of salmonid survival from the Klamath River, California, USA, 1980–2012.</p

Potential Factors Affecting Survival Differ by Run-Timing and Location: Linear Mixed-Effects Models of Pacific Salmonids (<i>Oncorhynchus</i> spp.) in the Klamath River, California

<div><p>Understanding factors influencing survival of Pacific salmonids (<i>Oncorhynchus</i> spp.) is essential to species conservation, because drivers of mortality can vary over multiple spatial and temporal scales. Although recent studies have evaluated the effects of climate, habitat quality, or resource management (e.g., hatchery operations) on salmonid recruitment and survival, a failure to look at multiple factors simultaneously leaves open questions about the relative importance of different factors. We analyzed the relationship between ten factors and survival (1980–2007) of four populations of salmonids with distinct life histories from two adjacent watersheds (Salmon and Scott rivers) in the Klamath River basin, California. The factors were ocean abundance, ocean harvest, hatchery releases, hatchery returns, Pacific Decadal Oscillation, North Pacific Gyre Oscillation, El Niño Southern Oscillation, snow depth, flow, and watershed disturbance. Permutation tests and linear mixed-effects models tested effects of factors on survival of each taxon. Potential factors affecting survival differed among taxa and between locations. Fall Chinook salmon <i>O. tshawytscha</i> survival trends appeared to be driven partially or entirely by hatchery practices. Trends in three taxa (Salmon River spring Chinook salmon, Scott River fall Chinook salmon<i>;</i> Salmon River summer steelhead trout <i>O. mykiss</i>) were also likely driven by factors subject to climatic forcing (ocean abundance, summer flow). Our findings underscore the importance of multiple factors in simultaneously driving population trends in widespread species such as anadromous salmonids. They also show that the suite of factors may differ among different taxa in the same location as well as among populations of the same taxa in different watersheds. In the Klamath basin, hatchery practices need to be reevaluated to protect wild salmonids.</p></div

Klamath River basin, California and Oregon (modified from Quiñones et al. 2013).

<p>Rectangles represent dams.</p

Climate Change Vulnerability of Native and Alien Freshwater Fishes of California: A Systematic Assessment Approach

<div><p>Freshwater fishes are highly vulnerable to human-caused climate change. Because quantitative data on status and trends are unavailable for most fish species, a systematic assessment approach that incorporates expert knowledge was developed to determine status and future vulnerability to climate change of freshwater fishes in California, USA. The method uses expert knowledge, supported by literature reviews of status and biology of the fishes, to score ten metrics for both (1) current status of each species (baseline vulnerability to extinction) and (2) likely future impacts of climate change (vulnerability to extinction). Baseline and climate change vulnerability scores were derived for 121 native and 43 alien fish species. The two scores were highly correlated and were concordant among different scorers. Native species had both greater baseline and greater climate change vulnerability than did alien species. Fifty percent of California’s native fish fauna was assessed as having critical or high baseline vulnerability to extinction whereas all alien species were classified as being less or least vulnerable. For vulnerability to climate change, 82% of native species were classified as highly vulnerable, compared with only 19% for aliens. Predicted climate change effects on freshwater environments will dramatically change the fish fauna of California. Most native fishes will suffer population declines and become more restricted in their distributions; some will likely be driven to extinction. Fishes requiring cold water (<22°C) are particularly likely to go extinct. In contrast, most alien fishes will thrive, with some species increasing in abundance and range. However, a few alien species will likewise be negatively affected through loss of aquatic habitats during severe droughts and physiologically stressful conditions present in most waterways during summer. Our method has high utility for predicting vulnerability to climate change of diverse fish species. It should be useful for setting conservation priorities in many different regions.</p></div