2000 Skagit River Wild 0+ Chinook Production Evaluation Annual Report

Skagit River chinook returns (spring and summer/fall combined) have steadily declined over the last fifty years (PSSSRG 1992) (PSSSRG 1997). In 1994, the Joint Chinook Technical Committee of the Pacific Salmon Commission designated the status of these stocks as �"Not Rebuilding.” To address this poor stock status, in 1995, resource managers formed the Skagit River Chinook work group. Composed of state, tribal, and federal fish biologists, this group recommends and coordinates restoration and monitoring programs. A major goal of this work group is to determine the factors of decline for chinook. Necessary data for this purpose include an indicator-stock tagging program, habitat inventory, annual adult escapement estimation, and wild juvenile chinook assessment. The juvenile production evaluation is a vital link in monitoring this stock’s population over time because it provides a direct measure of freshwater survival.

Seattle City Light (operators of several dams on the Skagit River), through a 1991 fisheries settlement agreement with WDFW, Federal agencies (NMFS, USFWS, USFS, and NPS), and the Skagit Tribes created the Skagit Non-Flow Plan Coordinating Committee (NCC). The NCC is responsible for funding several non-flow fisheries programs including the �"Chinook Research Program.” Beginning in 1997, this program provided funding to conduct chinook studies. This report documents our 2000 downstream migrant trapping project in the Skagit River which, with funding from the NCC, we conducted the fourth year of expanded monitoring of wild juvenile chinook production.

Understanding the major sources of interannual variation in run size is critical to improving harvest and habitat management. Quantifying anadromous salmonid populations as seaward migrants near saltwater entry is the most direct assessment of stock performance in freshwater because the variation resulting from marine survival and harvest are excluded. Relating smolt production to adult spawners over a number of broods empirically determines the watershed’s natural production potential (provided escapement and environmental conditions are sufficient), its stock/recruit function if escapements are less than that required to achieve maximum production, and enables identification of the major density-independent source(s) of interannual variation in freshwater survival. To accomplish these and other fish management objectives, the WDFW implemented a long-term research program directed at measuring wild salmon production in terms of smolts and adults in selected watersheds, in 1976 (Seiler et al.1981). In 1981, this program, which was directed primarily at coho salmon, was expanded to include additional large watersheds (Seiler et al.1984).

In 1990, we initiated downstream migrant trapping in the Skagit River system to quantify wild coho smolt production to, among other objectives, resolve a discrepancy in escapement estimates (Conrad et al 1997). This program, which in 2000 was in its eleventh year, involves trapping and marking wild coho smolts emigrating from a number of tributaries, and sampling a portion of the entire population via floating traps in the lower mainstem (R.M. 17, Burlington Northern railroad bridge). In addition, we continued to evaluate returns of coho adults coded-wire tagged as smolts at the gulper in Baker Lake. The upstream migrant trap below the dam provides a reliable accounting of all salmon returning to this system. Applying the marine survival estimated from the tag-based estimates of harvest and escapement to respective estimates of total system wild coho smolt production yields estimates of adult recruits, escapement, and harvest for the entire Skagit River system (Seiler et al.1995).

Although our trapping in the mainstem was initially directed at coho smolts, we identify and enumerate all fish captured. For the first seven years (1990-1996), season total 0+ chinook catches in the one scoop trap have varied six-fold, from 1,700 to 10,500 chinook. (As of 1993, we have simultaneously operated both a scoop and a screw trap.) In addition to abundance, these catch totals are influenced by fishing effort (the time fished on each date and for the season), migration timing relative to the interval we trapped, and instantaneous trap efficiency. Many such variables as discharge, water velocity, turbidity, debris, channel configuration, trap placement, and fish size combine to affect instantaneous trap efficiency.

Preliminary expansion of these 0+ chinook catches, based on the season average recapture rates of wild coho and several other assumptions held consistent between years, has yielded chinook production estimates that range from 0.5 to 6.4 million. The accuracy and precision of these estimates is presently incalculable because the assumptions remain unverified. We believe, however, that these estimates reflect the abundance of wild 0+ chinook production from these broods, at least in a relative sense. We base this contention upon the significant negative correlation between the freshwater survival estimates and the severity of flow during the period that the eggs were incubating in the gravel. The survival rates in this relationship are the ratio of total 0+ chinook emigrants estimated past the traps to the potential egg deposition. System total egg deposition is simply the product of the estimated total adult chinook escapement, an assumed even sex ratio and a fecundity of 5,500 eggs/female. This relationship indicates that overall eggto- migrant survival for Skagit River chinook has varied over ten-fold within just these ten broods, primarily as a function of flow during egg incubation.

In 1997, with funding from Seattle City Light, we began trapping in mid-February and continued into September. This season of extended trapping produced our first insight into the migration timing of wild chinook over nearly the entire migration interval. For the season, we estimated 4.5 million 0+ chinook.

Measuring the biological attributes of outmigration timing and size contributes to our understanding of juvenile chinook freshwater life history. This information is useful for flow management (dams and other flow controls), habitat protection, and designing hatchery programs to minimize hatchery/wild interactions.

We estimate coho smolt production from the Skagit River with the mark and recapture strategy that we developed and have used successfully in a number of large watersheds throughout the state over many years. This method involves the following components:

1. Trapping all the wild coho smolts emigrating from selected tributaries located throughout the basin;
2. Identifying each of these smolts with an external mark; and
3. Capturing a portion of the smolt population migrating through the lower mainstem and examining each fish for the mark.

This design produces relatively precise (CV<5%) and (we believe) unbiased production estimates, because a representative portion of the coho smolt population is marked at the tributary traps. Therefore, trapping in the mainstem does not have to be continuous or even representative with respect to timing (Seber 1982). We explicitly developed this design to avoid the requirement of estimating gear efficiency.

Because of the early life history characteristics of chinook in freshwater, estimating their smolt production with the same statistical precision we achieve for coho smolts is not possible. Chinook originate in discrete portions of the mainstem, and subsequently rear for variable intervals in various reaches. Therefore, the methodology we use with coho, capturing and identifying a representative portion of the entire population, is not feasible for chinook. Each population component likely has different survival patterns that result from the complex interactions of a number of factors: their parent's spawning timing and distribution; geneticallyprogramed juvenile rearing strategies; and the flow and habitat conditions each brood and subpopulation within it encounters. In a system as wide as the lower Skagit River, the migration pathways selected may also vary between sub-populations, which would affect capture rates. In addition to fish size and behavior, susceptibility of migrants to capture also varies as a function of flow and environmental conditions in effect upstream of the trap and at the trap.

Operating downstream migrant traps over an extended period in the dynamic environment of the lower mainstem of a large river is challenging when conditions are optimal. During the spring runoff, however, as flows and debris levels exceed some threshold, it becomes impossible. Above a certain discharge, capture efficiency is generally some negative function of flow. When the traps are inoperable, however, it is zero. For these periods, migration has to be estimated by interpolation. Such estimates are biased if smolt migration rates are affected by flow changes, which we believe they are.

Calibrating the traps in the lower Skagit River with wild chinook caught in the traps is not feasible; catches within a sufficiently narrow time strata are simply too low. While hatchery chinook offer the potential of sufficient release group sizes on some broods, the requisite assumptions that they survive, distribute vertically and laterally, behave, and consequently, are caught at the same rate as wild chinook, are unverifiable and therefore, problematic as well.

Sources of Variation Affecting Wild 0+ chinook Estimates

Given the foregoing problems, estimating wild juvenile 0+ chinook production from the trapping data we have collected in the lower Skagit River involves a number of assumptions. Accuracy of the resultant estimates are a direct function of the veracity of these assumptions. Each assumption deals with the uncertainty resulting from the following five major sources of variation we have identified.

1. Trap efficiency. Expanding catches to estimate wild 0+ chinook production requires estimates of instantaneous gear efficiency, ideally as a function of some measurable variable such as discharge.
2. Day vs night trap efficiency. Trap efficiency may be influenced by light. For example, it may be lower during the daylight than at night.
   
   We have operated the traps primarily at night because catch rates, especially for coho and to a lesser extent chinook, are higher at night than during the daylight. Estimating instantaneous trap efficiency during the daylight hours, however, is probably not possible because it would require that a sufficient and known number of marked wild chinook pass the traps within a single daylight period. The traps fish only the top 4 ft of the water column, and the depth at our site is 15-40 ft, depending on discharge. If, as a function of increasing light intensity, juvenile chinook migrate at greater depth and/or their ability to avoid the trap increases, then trap efficiency during daylight hours would be lower. The behavior of juvenile chinook and the biases imposed by releasing marked fish immediately upstream of the traps precludes estimating instantaneous efficiency within such a limited time interval as a single daylight period. Catches during daylight hours appear to be positively affected by turbidity. If true, this results either from increased migration rate and/or from an increase in trap efficiency because avoidance is reduced.
3. Day vs. night migration. Efficiency-based estimates rely on trapping either continuously or randomly throughout the time strata that migration is estimated. We developed our experimental design for estimating coho production to avoid the requirement of continuous trapping in the mainstem. Therefore, trapping in previous years was conducted almost entirely at night, when we capture coho smolts.
4. Migration interval. Skagit River 0+ chinook emigrate over a wider season than coho smolts. Chinook begin their downstream migration in January or earlier, and continue through the summer. In most years, we operated the traps over the coho smolt migration period, early-April through mid-June. Beginning in 1994, and continuing through 1996, we extended trapping longer, as late as mid-July. In 1997, we began trapping in mid-February and continued into September. To better define the early portion of the migration period, in 1998 and 1999, we began trapping in mid-January and extended trapping into September. In 1999 and 2000 we attempted to assess fall migration by operating the traps intermittently during October.
5. Incidence of hatchery-produced fish. Prior to 1994, releases of hatchery-produced 0+ chinook in the Skagit River were unmarked. Consequently, our estimates of wild chinook production for the first four years rely on an assumption for the number of hatchery-produced fingerlings we caught. Estimating both components of the migration relies on assumptions of how many hatchery fish survived to pass the trap during the interval trapped. Beginning with the 1993 brood, (released in 1994) all hatchery-produced zero age chinook released into the Skagit River have been marked with an adipose fin-clip (ad-mark) and coded-wire tagged.

Study Plan for 2000

The study plan for the 2000 trapping season was directed at continuing to improve the estimates of Skagit River chinook production through achieving a better understanding of the sources of variation. In addition to continuing our analysis of the chinook and coho trapping data collected over the previous eight years, the 2000 work plan included the following six operational elements.

1. Trapping season. A critical uncertainty in estimating Skagit River wild 0+ chinook production is their emigration timing. In 2000 we began trapping in mid-January and continued through mid-August, with intermittent sampling in September and October. We operated the screw trap one night in mid-September and over five days in October before removing the traps from the river on October 27.
2. Nightly trap operation. Nightly trapping with both the scoop trap and screw trap was continued throughout the season.
3. Daytime trap operation. Daytime trapping occurred every third day. We enumerated catches shortly after dawn and around dusk to enable separating day and night catches.
4. Right and left ventral-marking. To continue assessing a potential bias in our coho smolt production estimates, we continued differential fin-marking. As in 1999, we marked the smolts captured at Mannser Creek with a partial right ventral (RV) fin-clip. The National Park Service (NPS) continued marking the coho smolts they trapped in several upper tributaries with an LV-mark
5. Trap efficiency. In addition to the marked wild coho released from the tributary traps and the groups of hatchery fingerlings released from the two production facilities, we marked and released above the trap four groups of hatchery chinook, and four groups of dye-marked pink and chum fry.
6. Measuring visibility. To better understand the influence of water clarity on migration behavior, we measured visibility each day over the 2000 season. Visibility data will be correlated with flow and fish catch data.