2.1. Data used for trend analysis of salmonid escapement to the Klamath River, California. Run/Species Location Year Number of years analyzed Method Data analyzed Data source* Fall run Chinook salmon Klamath River basin 32 Carcass, redd, video weir and hatchery counts of adults and grilse ln(escapement) CDFG Klamath River basin – natural escapement 32 Carcass, redd, and video weir counts of adults and grilse ln(escapement) CDFG Bogus Creek – natural escapement 32 Carcass and redd counts of adults and grilse ln(escapement) CDFG Salmon River – natural escapement 32 Carcass and redd counts of adults and grilse ln(escapement) CDFG Scott River – natural escapement 32 Carcass, redd, and video weir counts of adults and grilse ln(escapement) CDFG Shasta River – natural escapement 32 Carcass, redd, and weir counts of adults and grilse ln(escapement) CDFG Trinity River – natural escapement 32 Carcass and redd counts of adults and grilse ln(escapement) CDFG Klamath River basin – % natural escapement 32 Carcass and redd surveys, video weir counts of adults and grilse natural spawners % of basin escapement as natural spawners CDFG Klamath River basin – 23 Coded wire tag recoveries and ln(escapment) CDFG2 2009 2009 2004 2009
hatchery strays production multipliers of adult and grilse natural spawners of hatchery origin Table 2.1. continued Iron Gate Hatchery 43 Adult and grilse returns to hatchery ln(returns) CDFG Trinity River Hatchery 28 Adult and grilse returns to hatchery ln(returns) CDFG Late fall run Chinook Salmon Blue – natural escapement 20 Stream survey peak counts of adults in reaches 1-4 ln(escapement) YTF Spring run Chinook salmon Salmon River – natural escapement 34 2 day snorkel survey counts of adults and grilse ln(escapement per km) KNF Trinity River Hatchery 26 and grilse returns to hatchery ln(returns) USFWS Trinity River – natural escapement 28 Adult and grilse escapement to areas outside Trinity River Hatchery ln(escapement) CDFG3 Coho salmon Iron Gate Hatchery 43 Adult returns to hatchery ln(returns) IGH Trinity River Hatchery 44 Adult returns to hatchery ln(returns) TRH Steelhead trout Iron Gate Hatchery 44 Adult (spring & fall) returns to hatchery ln(returns) IGH Trinity Hatchery 44 Adult returns to hatchery ln(returns) TRH Summer Steelhead trout Creek- natural escapement 25 1 day snorkel survey counts of adults ln(escapement per km) KNF Elk Creek – natural escapement 23 1 day snorkel survey counts of adults ln(escapement per km) KNF 34 KNF 1985-
Salmon River – natural escapement 2 day snorkel survey counts of adults ln(escapement per km) Table 2.1. continued Wooley Creek – natural escapement 22 1 day snorkel survey counts of adults ln(escapement per km) KNF Coastal cut- throat trout Blue Creek – natural escapement 9 Stream survey peak counts of adults in reaches 1-4 ln(escapement) YTF *CDFG = California Department of Fish and Game’s “megatable”, = M. Knechtle pers. comm. 2010, CDFG3 = (); YTF = Yurok Tribe Fisheries, KNF = Klamath National Forest, USFWS = United States Fish and Wildlife Service, IGH = Iron Gate Hatchery, TRH = Trinity River Hatchery Cross correlations Cross correlation is useful in evaluating the relationship between two time series (). Because we wanted to further investigate the relationship between natural escapement and hatchery supplementation, we conducted cross correlation between pairs of time series where both natural escapement and hatchery return estimates were available for the same taxa. The pairs evaluated were: Total numbers of fall Chinook spawners (natural escapement + hatchery returns) in the basin vs. fall Chinook returns to both hatcheries, spring Chinook natural escapement to the Salmon River vs. spring Chinook returns to TRH, spring Chinook natural escapement to the Trinity vs. spring Chinook returns to TRH, late fall Chinook natural escapement to Blue Creek vs. Chinook returns (both spring and fall runs) to TRH, and summer steelhead natural escapement to Salmon vs. steelhead returns to IGH.
Hatchery 2.2. continued Trinity River – natural escapement 0.83 0.0016 -0.51 1998.63 0.06 0.83 Salmon River – natural escapement 0.71 0.0046 -0.90 2000.37 0.06 0.71 Scott River – natural escapement 0.29 0.037 -2.41 2013.61 0.18 0.29 Shasta River – natural escapement 0.25 0.04 -2.08 2010.48 0.20 0.25 Bogus Creek– natural escapement 0.25 0.04 2.23 1974.11 0.20 0.25 Late fall run Chinook salmon Blue Creek – natural escapement 0.032 0.23 0.070 -135.21 0.59 0.032 Spring run Chinook salmon Salmon River – natural escapement 0.0013 0.28 0.055 -108.47 0.93 0.0015 Trinity Hatchery 0.00087 0.35 0.054 -98.88 0.95 0.00099 Trinity – natural escapement 0.27 0.047 0.023 -37.21 0.19 0.27 Coho salmon Iron Gate Hatchery 0.26 0.030 0.013 -19.51 0.20 0.27 Trinity River Hatchery <0.0001 0.47 0.09 -169.46 1.0 <0.0001
Table 2.2. continued Steelhead Iron Gate Hatchery 0.0004 0.30 -0.054 112.94 0.99 0.0004 Trinity River Hatchery 0.51 0.010 0.010 -64.09 0.77 0.51 Summer steelhead trout Clear Creek – natural escapement 0.19 0.072 -0.03 66.98 0.25 0.19 Elk Creek – natural escapement 0.68 0.0084 -0.01 21.80 0.07 0.68 Salmon River – natural escapement 0.00055 0.32 -0.063 125.62 0.96 0.00074 Wooley Creek – natural escapement 1985- 0.66 0.010 -0.015 31.00 0.07 0.65 Coastal cutthroat Blue Creek – natural escapement 0.10 0.33 0.11 -213.25 0.37 0.10
Figure 2.2. Trends in salmonid escapement for representative taxa in the Klamath River. In the upper graph, black stars represent time series data, black lines represent linear trendline (from permutations), dotted lines represent trend output, and broken lines represent intercept parameters. In the lower graphs, black bars represent posterior probabilites of step changes, gray bars represent posterior probabilites of trend changes, and the lines represent the odds ratio significant to each time series. Ch = Chinook, Sp Chinook = spring Chinook, l fall Ch = late fall Chinook, sthd = steelhead, s sthd = summer steelhead. Figure 2. 3. Percent of basinwide fall Chinook escapement comprised of natural escapement and hatchery returns, Klamath River, California, 1978-2009. Cross correlations Several natural escapement time series were significantly correlated to hatchery returns (Table 2.3). Basinwide fall Chinook adult spawner abundance was significantly correlated to returns to both hatcheries (r(27) =0.53, p = <0.05). Fall Chinook natural escapement to Bogus Creek was significantly correlated to returns to both IGH (r(27) = 0.60, p = <0.05) and TRH (r(27) = 0.58, p = <0.05). Fall Chinook natural escapement to Salmon River was significantly correlated to returns to IGH (r(27) = 0.36, p = <0.05). Fall Chinook natural escapement to Trinity River was significantly correlated to returns to both IGH (r(27) = 0.41, p = <0.05) and TRH (r(27) = 0.72, p = <0.05). Spring Chinook natural escapement to the Salmon River was significantly
conspecifics are likely replacing the wild populations of both taxa, raising concerns about the viability and persistence of wild stocks (Quiñones, unpublished data). Steelhead trout Steelhead are the anadromous form of rainbow O. mykiss. Two distinct life history patterns are recognized in the Klamath River basin: winter, and summer steelhead trout (). Winter steelhead trout move upstream after the onset of winter rains between November and April, shortly before spawning. Summer steelhead trout move upstream from April to June, spend the summer months in deep pools while they mature and spawn from December to April. Life histories differ in smolt age, length of marine residency, and patterns of reproduction (). Steelhead trout adults are capable of spawning once a year but often spawn every other year, up to four times. Most adults become reproductively mature from age 1 to 5 (). Juveniles will spend one to two years in cold fast-flowing perennial streams and are often associated with riffle habitats. Trends of adult Iron Gate Hatchery steelhead and Salmon River summer steelhead trout are in steep decline (Quiñones, unpublished data) and appear to be on the brink of extinction (). Figure 3.1. Klamath River basin, California and Oregon. Methods Conceptual To synthesize our hypotheses, we first constructed a conceptual model of variables potentially driving Pacific salmon abundances, based on peer-reviewed literature (discussed in the Introduction section; Figure 3.2). The variables were divided into three categories, those that affect internal population dynamics (population variables), climatic conditions (climate variables), and fresh water habitat quality (habitat variables). We recognize that factors interact with one another, within and among categories. Their interactions are investigated in our analysis described below. However, we organized the factors in the conceptual model to facilitate initial