Assessment of the Status of Oregon Populations of Natural Coho Salmon Spawners in the Lower Columbia River, 2002 E. T. Brown S

Assessment of the Status of Oregon Populations of Natural Coho Salmon Spawners in the Lower Columbia River, 2002

E. T. Brown S. E. Jacobs D. A. Kreager

Oregon Department of Fish and Wildlife 3406 Cherry Drive N. E. Salem, Oregon 97303

September 2003

This work was financed in part by the Columbia River Fisheries Development Program (Mitchell Act) administered by NOAA Fisheries, Project NA17FH1628.

CONTENTS

INTRODUCTION ...... 1

BACKGROUND ...... 1

MONITORING DESIGN...... 2

METHODS...... 5

RESULTS AND DISCUSSION ...... 6

Assessment of Survey Conditions...... 6

Spawn Timing ...... 8

Spawning Distribution...... 13

Coded-Wire Tag Recoveries ...... 15

Trends In Spawner Abundance ...... 17

Estimates of Spawner Abundance ...... 19

PLANS FOR 2003 ...... 22

ACKNOWLEDGEMENTS ...... 23

REFERENCES ...... 23

APPENDIX A...... 25

Randomly Selected Spawning Surveys, 2002 ...... 25

INTRODUCTION

Natural populations of coho salmon inhabiting the lower Columbia River (LCR) are listed as Endangered under the State of Oregon’s Endangered Species Act and are a candidate species for listing under the Federal Endangered Species Act (http://www.nwr.noaa.gov/1salmon/salmesa/cohoswwa.htm). The State of Oregon has developed a plan to recover populations of LCR coho inhabiting tributaries within the state (Chilcote 2003). This plan calls for enhanced efforts to monitor the status and trends of these stocks by providing rigorous annual estimates of spawner abundance. This work is intended to provide a framework for future adult spawner assessment and expansion of monitoring to include juvenile abundance estimates and habitat assessment beginning in 2003. This report describes work accomplished during the first season of enhanced spawner abundance monitoring.

BACKGROUND

Since 1949, peak counts from spawning fish surveys conducted in ten standard index areas have been used to assess trends of naturally spawning populations of LCR coho salmon. The geographic boundaries for each of these populations are presented in Table 1 and Figure 1. In addition to the index streams, supplemental surveys were conducted between 1959 to1974 to obtain a wider perspective on LCR coho escapement and productivity (Ollerenshaw 2003). Peak counts have trended downward since the early seventies, and in July 1999 the Oregon Fish and Wildlife Commission (OFWC) listed wild (naturally produced) LCR coho salmon as an endangered species.

Table 1. Lower Columbia River coho salmon population complex boundary descriptions.

Population Stream Spawn Complex Boundary Description Miles Miles

All Columbia tributaries from mouth upstream to, and Astoria 383 71 including, the Gnat Creek basin. All Columbia tributaries upstream of Gnat Creek to and Clatskanie 172 35 including the Clatskanie River Basin. All Columbia River tributaries upstream of Clatskanie Scappoose River to but not including the mouth of the Willamette 323 71 River The Clackamas River basin and all tributaries of the 704a 261a Clackamas Willamette River downstream of Willamette Falls 314b 116b All Columbia River tributaries upstream of the mouth of 431a 108a Sandy the Willamette River to and including the Sandy River 169c 21c basin. All Columbia River tributaries upstream of the Sandy Bonneville 325 8 River to and including the Hood River.

a Entire basin. b Downstream from North Fork Dam. c Downstream from Marmot Dam.

Six population complexes were tentatively identified as independent wild populations and provided the framework for a LCR coho Recovery Plan (Chilcote, 1999). Only two of these complexes, the Sandy and the Clackamas, were believed to harbor self- sustaining wild coho populations. In 2001 funds were appropriated to develop a systematic monitoring program to more comprehensively assess each of the complexes.

Figure 1. Geographic boundaries of the six population complexes for coho salmon in the lower Columbia.

MONITORING DESIGN

The monitoring design for LCR coho was based upon the design developed and used for coastal Oregon coho salmon monitoring efforts (Jacobs et al., 2002), which utilized the U.S. Environmental Protection Agency’s Environmental Monitoring Assessment protocol (EMAP) (Stevens, 2002). The selection frame was created by adapting Stream Net’s 1:1000k Geographic Information System (GIS) coho coverage (http://www.streamnet.org) to identify coho spawning and rearing habitat. Figure 2 depicts the coverage used as a sampling frame. Potential survey sites were selected following EMAP protocol with the goal of establishing 90 spawning survey sites over the entire study area. Points were geographically balanced within each of the six complexes. To allow for contingencies, 124 sites were selected. The geographic locations of randomly selected sites and their outcomes are illustrated in Figure 3. Landownership was determined using County assessors’ databases to reconcile site maps with tax lot information. In cases of absentee or corporate ownership, permission request letters were mailed. In June, biologists

assessed selected sites to determine habitat quality and accessibility. All landowners on those sites deemed suitable were contacted. Upon receiving landowner permission, verification crews conducted additional assessments to ensure survey validity in accordance with the Coastal Salmonid Inventory Project protocol (Jacobs and Nickelson, 1998). Spawning survey signs were placed at the boundaries of each survey, and a description was written which included maps and a database of site statistics and information. Landowner information was similarly entered into a database.

Figure 2. Map (1:100K) of sampling frame showing areas considered to be coho salmon spawning habitat for the lower Columbia. Some of the1:24K stream reaches selected as spawning habitat included in the sampling frame are not depicted. Spawning habitat upstream from dams is not included in the sampling frame.

Ninety of the 124 selected sites (72%) were ultimately verified as suitable for inclusion in the sampling (Table 2 and Appendix A). The geographic distribution of verification sites and their status is shown in Figure 3. The database of spawning habitat and GIS coverage of spawning distribution was revised to reflect the results of field verification. An additional ten standard surveys and one supplementary survey were added to the sample to continue trend information, and are detailed in Table 3.

Table 2. Spawning survey site selection by population complex, 2002.

Population Spawning Potential Sites Sites Standard Complex Miles Sites Verified Dropped Sites

Astoria 71 27 15 12 2 Clatskanie 35 18 16 2 2 Scappoose 71 28 22 7 4 Clackamas 116 41 29 11 2 Sandy 21 5 4 1 0 Bonneville 8 5 4 1 1a

Total 322 124 90 34 11 a Supplemental survey site.

Figure 3. Outcome of summer of 2002 site verification. Sites that were classified as dropped, inaccessible, or access denied were not surveyed in 2002 but may be randomly selected in the future. Sites that were classified assumed zero are thought to include no spawning habitat, and will be excluded from future site selection.

Table 3. Standard and supplemental surveys conducted in the Lower Columbia River, 2002.

Seg- Subasin Reach ID ment Survey Name Type Miles

Main Stem 30089.00 2 Youngs River Standard 0.3 Main Stem 30171.00 3 Little Creek Standard 1.2 Main Stem 30303.00 1 Carcus Creek Standard 1.3 Upper Clatskanie River Main Stem 30308.50 2 Standard 0.9 (Wilark Unit) Milton Creek 30802.00 2 Salmon Creek Standard 0.3 Milton Creek 30803.00 3 Milton Creek Standard 0.3 S. Scappoose Cr. 30824.00 1 Raymond Creek Standard 1 Sierks Creek N. Scappoose Cr. 30831.00 1 Standard 0.3 (Deep Creek) Main Stem 30896.00 2 Tickle Creek Standard 1.6 Main Stem 30901.00 4 Deep Creek Standard 2 Multnomah Creek 33607.00 1 Multnomah Creek Supplemental 0.1

METHODS

Surveys were divided geographically between two two-person crews based in Astoria and Sauvie Island, and one three-person crew based in Clackamas. Surveys were performed within a ten-day rotation, beginning in the second week of October and ending in the third week of January (after two consecutive weeks of zero live counts). Live coho observations were tallied as fin-clipped (adipose), unmarked, unknown mark adults; or as jacks (< 43 cm MEPS length). Information on recovered carcasses was tallied as males, females or jacks. All carcasses were sampled by recording date, location, species, sex, MEPS length and fin-clips. All carcasses were sampled for scales, and all unmarked coho (those with intact adipose fins) had fin rays removed for DNA analysis. Marked carcasses (those with clipped adipose fins) had snouts removed to recover coded-wire tags (CWT), except at specific sites located in the Astoria, Clackamas and Bonneville complexes, where large numbers of marked coho necessitated using snout wands. Tails of all sampled carcasses were removed, and previously handled carcasses were tallied by adult or jack.

Except in the Sandy and Bonneville complexes, hatchery: wild ratios were estimated in each complex by calculating the ratio of marked to unmarked carcass recoveries, then adjusting mark rates with the rate of marked returns to area hatcheries, as follows:

Pi = Ai /( Ci Ri ) (1) where,

Pi = Estimated proportion of hatchery-origin spawners to total natural spawners in population complex i.

Ai = Number of adipose-clipped carcasses recovered in population complex i.

Ci = Total number of carcasses recovered in population complex i

Ri = Proportion of smolts released from hatchery facility in population complex i that was adipose fin-clipped.

Hatcheries within complexes closest to and having the greatest potential for effect on ratios and that were used in calculations were: Big Creek (Astoria and Clatskanie), Eagle Creek (Clackamas), Cascade (Bonneville), and Cedar Creek (Sandy). The apparent straying of large-numbers of unmarked hatchery coho into Bonneville complex streams necessitated the use of scale analysis to estimate hatchery:wild ratios in that complex. The small number of carcasses recovered in the Sandy complex dictated the use of observations of live fin-marked coho to calculate hatchery: wild ratios.

Population estimates in the survey sites were calculated using Area-Under-the- Curve (AUC) techniques (Beidler and Nickelson 1980). Geographic strata population estimates were computed using the methods developed by Stevens (2002). The application of this technique to spawner surveys is described in Jacobs et al. (2002). The finite population correction (Cochran 1977) was used in calculating confidence intervals.

RESULTS AND DISCUSSION

Assessment of Survey Conditions

Figure 4 illustrates flow conditions in representative streams in the Lower Columbia region. Also shown is the mean daily flow in the Nehalem River for the 60-year period between 1943 and 1996. While the magnitude of peak flows was typical, the arrival of the first major freshet was much later than normal, arriving on 12 December in most basins. After this date a series of winter storms maintained winter flows at expected levels.

Lower Columbia coho typically spawn from November through early January. As a result of the late arriving rains which were exasperated by historically low summer and fall flows, portions of the spawning habitat normally available to coho throughout November were unavailable in smaller tributaries. A small freshet occurred in early November that brought coho into larger streams. In mid-November small numbers of coho were observed spawning in mainstem environments thought to be outside normal spawning range in the Lewis and Clark, Clackamas and Sandy Rivers, ostensibly due to lack of access to smaller (first and second order) streams. Generally, the smaller streams were not accessible until the second week in December, when a consistent series of freshets provided access to all sites, making survey schedules difficult to manage in some basins.

Hood River at Tucker Bridge 2000

1600

1200

800 Flow (cfs) 400

0 10/1/2002 10/31/2002 11/30/2002 12/30/2002 1/29/2003

Nehalem River at Foss 12000

Mean Daily Flow

8000 1943-96 Mean Daily Flow

Flow (cfs) 4000

0 10/1/2002 10/31/2002 11/30/2002 12/30/2002 1/29/2003

Naselle River 20 Mean Daily Flow Flood Stage Blown out 16

Stage in Feet 4

0 10/1/2002 10/31/2002 11/30/2002 12/30/2002 1/29/2003

Figure 4. Flow regime for the 2002-03 spawning season in Lower Columbia streams.

The Astoria and Clatskanie complexes received a moderate freshet in the second week of November, providing fish access to most of the second order streams. Survey schedules were easily maintained throughout November and early December. The 12 December freshet marked the beginning of a protracted series of flow events that made survey schedules more difficult to maintain through the first week in January. This was particularly true for the Clatskanie complex, where a sharp peak in coho counts coincided with a large flow event. Flows were low in the Scappoose complex until the second week of December. A period of continuously high flows occurred in the region in late December and early January, and survey schedules were maintained with moderate difficulty. The same was true for the Clackamas, Sandy and Bonneville complexes, except in the Johnson Creek subbasin, where consistently high turbidity associated with winter flows made survey schedules especially difficult or impossible to maintain.

The flow regime encountered during the 2002 spawning season was advantageous to the methods employed. Coho generally spawn in first to third order tributaries. Accordingly, our survey sites were restricted to these sites. Low flows provided good conditions to observe fish, and survey schedules were rarely interrupted. However, the extremely low flow regime that persisted throughout the early part of the season may have affected both the temporal and spatial distribution of coho salmon spawning by preventing spawners from accessing some of the low order tributaries. This situation may have resulted in a negative bias in estimates of spawner abundance. It also may have merged some of the populations of hatchery and wild runs normally thought to have temporally distinct peaks into overlapping peaks in early December.

Spawn Timing

Spawn timing is illustrated in Figure 5 for each of the six LCR complexes based on observation of live adults. Spawning in the LCR occurs primarily in November and December but can extend into January. LCR coho are assumed to spawn during two distinct peaks: hatchery populations in middle or late November and wild populations in mid-December (Ollerenshaw 2003). The lack of representative historical timing data makes comparison to past spawn timing difficult, however, the data that has been collected supports this assumption. Figure 6 suggests that spawning across the LCR may have occurred somewhat later in 2002 than normal, with a much higher percentage of total spawners observed in peak counts occurring in December than for the average of four previous years where spawn timing data are available (1991-93 and 2001).

60 Astoria 40

0 80 1591317 Clatskanie 60

0 60 1591317 Scappoose 40

0 40 1591317 Clackamas 30

10 Live Adult Coho Spawners (%) 0 60 1591317 Sandy 40

0 40 1591317 Bonnevile

0 October November December January February

Figure 5. Temporal distribution of spawning coho salmon within each population complex during the 2002-03 season. Values represent the percentage of live adults observed in all random survey segments.

100 90

80 November 70 December 60 50 40 30 20 Percent of Spawners Counted 10 0 Four-Year Average 2002

Figure 6. Percentage of LCR spawners observed during peak counts in November and December. The four-year average incorporates data from 1991-93 and 2001. A total of 201 coho spawners were observed in 2001 and the average number of spawners for the four-year period was 157.

The Astoria complex experienced a distinct peak spawning period around 7 November, with most fish observed in large order streams near the Klaskanine and Big Creek Hatcheries. Low flows in November kept coho out of smaller order streams, with spawning continuing through the second week of November and tapering off in the third week of the month. A final, relatively small peak occurred near the end of November. No further pronounced periods of spawning activity were observed in December or January. As predicted by the 7 November peak date, the count was composed primarily of marked fish. Approximately 4% of the spawners were composed of unmarked fish ostensibly due to a combination of hatchery mark rates (99%) in the Astoria complex and natural production of hatchery strays.

Clatskanie spawn timing reflected two distinct peaks, the first and smaller peak occurred on 14 November. The second and higher peak occurred 17 December, and dropped dramatically by 20 December, ending the season (Figure 5). The two peak periods fit the conventional model of the timing for hatchery and wild coho spawning in the Lower Columbia area.

Spawn timing in the Scappoose complex was similar to that of the Clatskanie both temporally and in relative magnitude, with a moderate peak occurring in the second half of November, and a second, more abrupt peak occurring 21 December and tapering off through early January. No marked live or dead coho were observed so the population was

assumed to be completely wild. However, the first spawning period was followed by a relatively long inactive period that appears indicative of a naturally reproducing hatchery population, followed by a wild population in December. Releases of hatchery stock in the area ended in the 1990’s, and the November peak may be a remnant of this former management practice.

Spawn timing in the Clackamas complex is similar to that in the Astoria complex, with a relatively long period of early spawning beginning 31 October and peaking on 11 November. Spawning activity after this date was minimal, steadily declining until 1 December with a very small peak occurring around 19 December.

Spawn timing in the Sandy complex assumed a unique pattern when compared to the other LCR Complexes, with the largest peak occurring in early December. Peak spawning in this complex occurred at a time of low spawning activity in most of the other five LCR complexes. Spawn timing data from supplemental surveys in the 1992-93 seasons suggested a very similar pattern (Figure 7). However, spawning in that period was initiated earlier, probably as a result of higher stream flow than what occurred in 2002.

0 Live Adult Coho Spawners (%) October November December January February

Figure 7. Spawn timing in supplemental surveys in the Sandy population complex for the 1992-93 spawning seasons.

Coho salmon in the Bonneville complex exhibited the most protracted period of spawning activity in the region. Spawning began 31 October and continued into the first week of January.

It appears that wild fish occurred across the region during the entire duration of the spawning season. Figure 8 illustrates that recoveries of wild carcasses were relatively equivalent in both November and December. Furthermore, scale analysis in the Bonneville complex (where mark rates of hatchery fish were difficult to account for) display similar percentages of wild spawning in both November and December. This suggests that natural reproduction is occurring throughout the lower Columbia study area somewhat uniformly in

both months, and brings to question the validity of the procedure of using a cut-off date of 1 December to distinguish hatchery and wild populations. Further incriminating the assumption of a temporal separation are the results displayed in Figure 6, which show that the 2002 spawning year varied from other years. This implies that using a fixed date to separate hatchery from wild populations may not provide a consistent index between years. This issue is illustrated in Figure 9, which compares the proportion of wild spawners in the total population estimated by the two methods: the 1 December cut-off date and the use of carcass recovery fin mark rates, corrected by local hatchery mark rates. This figure shows that hatchery:wild ratios estimated by each method can vary dramatically. For example, in the Bonneville complex, large numbers of spawners in December were shown through scale analysis to be of hatchery origin. Comparison with ratios from the Scappoose complex indicate approximately 60% of the population is wild using the cut-off date and 100% is wild using fin-mark rates, suggesting that the 1 December rule may predict stock origin rather than hatchery-wild proportions. The potential for variability shown by 2002 spawn timing data independently seems to question the use of 1 December as an index tool, and the natural reproduction of hatchery origin coho common throughout all of the lower Columbia makes it seem an obsolete method of estimation.

100%

80% November 60% December

40% Percent Wild

20%

0% Astoria Clatskanie Scappoose Clackamas Bonneville Population Complex

Figure 8. Proportion of naturally spawning adult coho in November and December 2002 estimated to originate from wild production by individual population complex.

100%

80%

Hatchery Wild 60%

40%

20% Naturally Spawning Coho

0% Astoria Clatskanie Scappoose Clackamas Sandy Bonneville Population Complex

Figure 9. Comparison of hatchery: wild ratios of naturally spawning coho in the LCR population complexes for 2002. For each population complex the first bar illustrates the hatchery: wild ratio as determined by applying a 1 December cutoff date. The second bar illustrates this ratio as estimated either by fin-mark recoveries or scale analysis.

Spawning Distribution

Densities of live coho observed in individual LCR random surveys conducted during the 2002-spawning season are displayed in Figure 10. This figure shows that the largest concentrations of coho occurred relatively near coho hatchery locations, but also demonstrates that coho spawning occurred across the entire study area, including streams remote from immediate hatchery proximity.

AS T$ O R IA # # # # # # r # ÚÊ # r r ## # # ÚÊ $ r # r r RAINIER # r # r # # r r # r r r # r r r # r # r ##$ ÚÊ Ha t c h e r i e s # $ STHELENS Ci t i e s # r# Ob s e r v e d f i s h p e r m i l e # # r 0 HO O D R $IV E R # # 1 - 1 0 # ÚÊ # ÚÊ 11 - 2 5 # # 26 - 1 0 0 # # $ 101 - 2 50 r r r PORTLAND # r r ## # 25 1 - 4 7 2 # # Po p u l a t i o n C o m p l e x e s # # # ÚÊ$ r r SANDY r # rr # # # r# r r r# # ÚÊ ## N

W E

Figure 10. Densities of naturally spawning coho salmon observed on Oregon tributaries of the lower Columbia River, 2002.

Wild coho occurred in all the complexes in the region, with the largest proportions (100%) of wild observed in the Scappoose complex (Figure 11). These results differ from the assumption in the original Recovery Plan’s estimation (Chilcote 2003) that wild fish occur only in the upper portions of the Clackamas and Sandy complexes. Random survey sites in the Clatskanie and lower Clackamas (Clear Creek) complexes were also dominated by wild fish.

AS T O R I A $ # # # # S# # S# # ÚÊ S# # # # #ÚS#Ê # # $# RAINIER # S# # S# #S #S # #S #S # ## # # # #

# # #

# #S# #S ÚÊ # #S#S$ Co h o Ha t c h e r i e s #S ST H E L E N S $ Ci t i e s #S #S# #S#S Ha t c h e r y : W i l d HO O D R I V E R # $ S# No Data ÚÊ # ÚÊ# 1- 1 0 % Wi l d S# S# 11 - 25 % Wi l d $ #

PO R T L A N D # S# # # # # 26 - 50 % Wi l d # # #S S#

51 - 99%Wild # # S# #S S# S# ÚÊ$ SA N D Y 10 0 % Wi l d # # # # # S# # #S# # S# Po p u l a t i o n Co m p l e x e s #S # # #S # ÚÊ #S#S

W E

Figure 11. Proportion of natural coho spawners that were estimated to be of wild origin on individual random spawning surveys, 2002.

Coded-Wire Tag Recoveries

Twenty-three CWT’s were recovered from coho carcasses sampled on spawning surveys (Table 4). All but one of these CWT’s were recovered from surveys located in the Astoria complex. The remaining CWT coho was recovered in Viento Creek in the Bonneville complex.

CWT recoveries suggest that hatchery straying was generally localized, with most hatchery fish spawning near their point of release. In the Astoria complex, 21 of the 22 CWT recoveries originated from releases in this complex. Furthermore, most of these recoveries occurred in the same stream where the release site was located. The one long- distance hatchery stray in the Astoria complex originated from the Little White Salmon National Fish hatchery which is located just upstream of Bonneville Dam.

The single CWT sampled in the Bonneville complex was the only tag found outside of the Astoria complex. The proportion of stray hatchery fish are particularly in question in this complex, where the proportion based on observed fin mark rates (43%) does not match

that calculated by scale reading (11%). This discrepancy is most likely due to straying of hatchery fish released upstream of Bonneville Dam, whose mark rates at around 27% were well below the 97% marked below Bonneville Dam (Oregon Production Index Technical Team’s table of yearling releases of mass marked coho). Because of insufficient CWT data in the Bonneville complex, scale-reading results were used to calculate hatchery:wild ratios for this complex.

No CWT recoveries were made in the Sandy complex, resulting in an inability to determine the origin of hatchery strays. There was only one carcass recovered, forcing the use of live marked observations as the calculation for hatchery:wild ratios.

Reasons for low tag recovery rates are unclear but may be attributed to use of snout wands which were relied upon in areas of high hatchery influence, particularly around Big Creek in the Astoria complex, Eagle Creek in the Clackamas complex, and all of the Bonneville complex streams. Astoria complex CWT recoveries (22) were three times the expected amount, however CWT recoveries in the Clackamas and Bonneville complexes were fewer than expected. Whether this is a result of improper use of the wands, wand malfunction, or poor recovery of coho with CWT’s is unclear.

Table 4. Hatchery-reared coho possessing coded-wire tags that were recovered on lower Columbia River spawning surveys, 2002.

Release Recovery Brood Release Recovery Tags Hatchery Location Location Year Year Date Recovered

Astoria Population Complex

Youngs Bay Net Klaskanine R. Klaskanine R. 2000 2002 12/6/02 2

Youngs Bay Net Klaskanine R. Klaskanine R. 1999 2001 12/6/02 1 Eagle Cr. Youngs Bay Youngs R. 1999 2001 12/6/02 1

Big Cr. Big Cr. Youngs R. 1999 2001 12/6/02 1

Oxbow Cr. Columbia R-1 Youngs R. 1999 2001 12/6/02 1 Tongue Pt. Oxbow Cr. Bear Cr. 1999 2001 11/22/02 (Astoria) 1 Big Cr. Big Cr. Little Cr. 2000 2002 11/22/02 1

Big Cr. Big Cr. Little Cr. 1999 2001 11/22/02 1 Tongue Pt. Oxbow Cr. Little Cr. 1999 2001 11/27/02 (Astoria) 1 Big Cr. Big Cr. Big Cr. 1999 2001 11/4/02 3

Big Cr. Big Cr. Big Cr. 1999 2001 11/5/02 2

Table 4. Continued.

Release Recovery Brood Release Recovery Tags Hatchery Location Location Year Year Date Recovered Big Cr. Big Cr. Big Cr. 1999 2001 11/23/02 3

Youngs Bay Net Klaskanine R. Big Cr. 1998 2000 11/23/02 1 Big Cr. Big Cr. Big Cr. 1999 2001 12/3/02 1 Little White Willard Big Cr. 1999 2001 11/4/02 Salmon R. 1

Bonneville Population Complex

Little White Willard Viento Cr. 1999 2001 12/3/02 Salmon R. 1

Trends In Spawner Abundance

Since 1949, ten standard spawning ground surveys have been conducted targeting coho salmon in Lower Columbia tributaries to index historical escapement. Since 1984, coho spawning prior to 1 December were assumed to be naturally spawning hatchery fish, therefore only peak counts occurring on or after this date were summarized. Table 5 displays the peak counts and AUC’s of the ten standard surveys and one additional supplemental survey, organized by population complex.

Standard coho spawning ground counts for 2002 at nine fish per mile were up slightly when compared to the previous 30 years. This count is similar to results occurring in 1980 and 2000, but still below both the 54-year average of 12 fish per mile and the average of 25 fish per mile established prior to the population declines that began in 1971 (Figure 12).

Table 5. Results of standard surveys for coho salmon spawners conducted in 2002.

Peak Count per Escapement milea (fish/mile)b Per Population Complex Survey Stream Adults Jacks AUC mile

Astoria Youngs River 13 27 77 257 Little Creek 2 0 13 11 Clatskanie Carcus Creek 3 2 6 5 Upper Clatskanie River (Wilark Unit) 0 0 0 0 Scappoose Salmon Creek 27 3 9 30 Milton Creek 20 0 6 20 Raymond Creek 7 0 8 8 Sierks Creek (Deep Creek) 137 3 41 137 Clackamas Tickle Creek 2 1 51 32 Deep Creek 2 0 5 3 Bonneville Multnomah Creek 130 0 74 740 a Excludes fish counted prior to 1 December. b Derived from area-under-the-curve estimates.

80.0

Peak counts

60.0 1972-2002 avg. 1949-2002 avg

1949-1971 avg. 40.0

20.0

0.0 1945 1955 1965 1975 1985 1995 2005 Year

Figure 12. Trend of coho peak counts in the ten LCR standard surveys from 1949 to 2002, including averages of three periods within this 54-year history. Counts prior to 1 December of each spawning season from 1984 to 2002 are not included.

The single supplemental survey performed in Multnomah Creek has only a five-year history, beginning in 1991 and running through 2002, but excluding 2000. The peak count for 2002 was at 12 fish per mile, which was double the previous high peak of 6 fish per mile in 1991 (Figure 13). Peak counts for standard surveys in 2000 were similar to 2002 counts, and it seems likely that this would hold true for the missing year of 2000 for this survey as well.

0 1990 1991 1992 2001 2002 Year

Figure 13. Peak counts of adult coho in the supplemental survey on Multnomah Creek for 1990-92 and 2001-02. No fish were observed in 2001. Peak counts are for dates after 1 December for each spawning season.

Estimates of Spawner Abundance

Estimates of LCR spawning escapement and associated 95% confidence intervals from 2002 random spawning surveys are presented in Table 6. Variability in survey-based estimates was high, creating relatively large confidence intervals. Across all complexes, the precision of the estimates of total and wild spawner escapement was within about + 35% of the point estimate. For individual complexes precision ranged from +37% to + 141%. Whether this is due to a consistent geographic variability inherent to the fish distribution in the region, or caused by low flow regimes and lack of access to smaller LCR streams is unclear.

The total estimate adult spawner escapement for the whole of the LCR region, including counts of adult coho passing upstream from dams or falls, are shown in Table 7. Total LCR coho spawner escapement for the six populations in 2002 is estimated at 10,529 coho, with an estimated total of 2,937 (28%) wild and 7,592 (72%) hatchery fish. These estimates include all areas considered to be within coho spawning distribution in the Lower Columbia area. Details of estimates for individual complexes are as follows:

Table 6. Estimates of coho spawner abundance for population complexes within the lower Columbia River, 2002. Estimates derived from counts in randomly selected spawning surveys.

Adult Spawner Abundancea Survey Effort Total Wildb Number 95% 95% Population Spawning of Confidence Confidence Complex Milesc Surveys Miles Estimate Interval Estimate Interval Astoria 71 15 15.94,473 2,792 386 241 Clatskanie 35 16 13.9 229 165 94 68 Scappoose 71 21 20.2 458 172 458 172 Clackamasd 116 30 33.5 2,402 1,471 576 353 Sandye 21 4 3.4 271 416 8 13 Bonneville 8 4 1.0 1,231 1,099 132 94

Total 322 90 87.19,064 3,225 1,654 612 a Estimates derived using EMAP protocol and adjusted for visual observation bias. b Estimates of wild spawners derived through application of fin-mark recoveries in random survey sites, except in the Sandy complex where observations of live fin-marked fish were used and in the Bonneville complex where results of scale analysis were applied. c Estimates derived from multiplying sample weight by number of survey sites in each complex. d Excludes spawning habitat upstream of North Fork Dam. e Excludes spawning habitat upstream of Marmot Dam.

Table 7. Counts of adult coho salmon passing upstream of dams located on tributaries of the lower Columbia River, 2002

Population Complex (Dam Site) Hatchery Wild Total Percent Wild Scappoose (Bonnie Falls) 0 68 68 100 Clackamas (North Fork) 123 878 1,001 88 Sandy (Marmot) 0 310 310 100 Bonneville (Powerdale) 59 27 86 67 Total Upstream from Dams 182 1,283 1,465 89

Overall Totala 7,592 2,937 10,529 28 a Total of passage counts and survey estimates.

Astoria complex

Estimates for coho in the Astoria complex were 4,473 total adults, of which an estimated 386 (8.5%) were wild. The high proportion of hatchery fish in this complex is at least partially attributed to the large numbers of smolt releases in this area.

Clatskanie complex

Estimates for coho in the Clatskanie complex were 229 total fish, of which an estimated 94 (41%) were wild. Peak flows may have obscured a portion of peak spawning in some subbasins, and estimates may be somewhat below actual spawner abundance. The small sample size of carcass recoveries (n= 17) may have affected the accuracy of the hatchery:wild ratio.

Scappoose complex

Estimates for coho in the Scappoose complex were 526 total fish, all of which were estimated to be wild. About 38% of these are potentially derived from a hatchery stock whose releases ended in the early 1990’s.

Clackamas complex

Estimates for coho in the Clackamas complex were 3,403 total fish, of which an estimated 1,454 (42.7%) were wild. Wild fish were located primarily above North Fork Dam where 88% of the 1,001 total fish passed were wild, and in Clear Creek where approximately 99% of the estimated 63 fish were wild.

Sandy complex

Estimates for coho in the Sandy complex were 581 total fish, of which an estimated 318 (54.7%) were wild. No hatchery fish were allowed passage at Marmot dam, but an estimated 310 of the 318 wild fish in the Sandy population were passed at this facility. Only four sites were surveyed in this complex, and this small sample size may have affected the accuracy of estimates for areas below Marmot dam.

Bonneville complex

Estimates for coho in the Bonneville complex were 1,317 total fish, of which an estimated 159 (12.1%) were wild. Eighty-six of these fish were above Powerdale Dam on Hood River. The presence of unmarked hatchery fish in the population complicates hatchery:wild ratio calculations, and the ratio results of scale reading were utilized for this complex only.

PLANS FOR 2003

This was the first year of systematic random sampling of coho spawners in the Lower Columbia region. We are planning to continue this sampling in 2003. For 2003 a number of changes will be made to improve the quality of the results:

Redefinition of habitat frame

In the spring of 2003, the habitat frame created for selection of survey sites was refined to include areas above the dams on both the Clackamas and Sandy Rivers. In this process, the preexisting habitat coverage was edited to represent the most current information on coho distribution within the whole of the Lower Columbia. All database tables were reconciled with this coverage, and are now linked to provide immediate modification as verification or changes in habitat status occur.

Expansion of survey areas to include stream reaches above dams

Survey sites for 2003 include stream reaches above the Marmot Dam on the Sandy River and the North Fork Dam on the Clackamas River to provide a better understanding of distribution, to aid in calibration of survey methods, and to prepare for monitoring that will be needed after the removal of Marmot Dam. This expansion adds a fourth survey crew and an estimated 30 sites to the overall sample. In addition, a crew leader will be added to aide supervision and data collection throughout the Lower Columbia region.

Site verification

For verification, 180 sites have been selected across the region to yield a total of 120 random surveys. Verification crews will spend three months to contact landowners and verifying site feasibility and suitability. Landowner lists and site information packets have been developed for the verification season.

Addressing small sample sizes

Only one site was selected in the Bonneville complex for 2003 verification. A sample size of four surveys in 2002 was insufficient for population assessment given its limited survey length of eight miles. Surveys throughout the total extent of spawning in this complex are being considered.

Hatchery:wild analysis and CWT recoveries

Small sample size of CWT recoveries for 2002 made assessment of straying difficult. Rectification of this problem, particularly in the Bonneville complex, is an goal for 2003. All carcasses recovered in the Clackamas, Sandy and Bonneville complexes will be sampled for coded wire tags using wands, regardless of presence of fin-marks. Wands will be tested prior to use.

Additional programs beginning in 2004

In addition to the random coho spawner surveys, an integrated program will begin in 2004 to include steelhead spawning surveys and habitat and juvenile salmonid monitoring. These programs will follow the protocol of the coastal monitoring efforts in Oregon (Stevens 2002), and will include overlapping survey sites.

ACKNOWLEDGEMENTS

We appreciate the hard work and diligence of our spawning survey crew: Bill (Wilt) Chamberlain, Tanna Clark, Tiffany Hughes, Jennifer Kauffman, Sarah Lyon, Casey Meyers and Chris Rodriguez. We also would line to thank the following individuals for helping make this effort possible:

Dave Sahagian, Scappoose Bay Watershed Council John Bowers, Johnson Creek Watershed Council Karen Streeter, Clackamas County. Todd Cullison, Astoria Watershed Coordinator Darlene Siegel, ODFW STEP Biologist, Clackamas Terry Otto and Chuti Fiedler, USFS Mark Nebeker, Manager at Sauvies Island Wildlife Refuge CRM, Clackamas and Astoria McKenzie Murray at OSU Printing Lisa Borgerson, ODFW Scale Analysis Loren Jenson, Bonneville Hatchery Alan Meyer, Manager Big Creek Hatchery Bill Murray, ODFW CWT Laboratory

REFERENCES

Beidler, W.M. and T.E. Nickelson. 1980. An evaluation of the Oregon Department of Fish and Wildlife standard spawning survey system for coho salmon. Oregon Department of Fish and Wildlife. Information Reports (Fish) 80-9. Portland.

Borgerson, L. 2003. Personal interview on 27 March , Oregon Department of Fish and Wildlife, Research and Development Section, Corvallis, Oregon.

Chilcote, M. W. 1999. Conservation status of lower Columbia River coho salmon. Oregon Department of Fish and Wildlife, Fish Division Information Report 99-3. Portland, Oregon.

Chilcote, M. W. 2003. Oregon Department of Fish and Wildlife’s endangered species management plan for lower Columbia River coho salmon. Fish Division. Oregon Department of Fish and Wildlife. Portland, Oregon.

Cochran, W. G. 1977. Sampling Techniques. John Wiley and Sons, New York.

Jacobs S.E. and T.E. Nickelson. 1998. Use of stratified random sampling to estimate the abundance of Oregon coastal coho salmon. Oregon Department of Fish and Wildlife, final reports (fish) Project # F-145-R-09, Portland.

Jacobs et al., 2002. Status of Oregon coastal stocks of anadromous salmonids, 2000- 2001 and 2001-2002; Monitoring Program Report Number OPSW-ODFW-2002-3, Oregon Department of fish and Wildlife, Portland, Oregon.

Ollerenshaw, E. 2003. 2001 Oregon lower Columbia River coho spawning ground surveys and 2002 coho juvenile survey results. Oregon Department of Fish and Wildlife, Columbia River Management.

Stevens, D.L. 2002. Sampling design and statistical analysis methods for integrated biological and physical monitoring of Oregon streams. OPSW-ODFW-2002-07, Oregon Department of Fish and Wildlife, Portland, Oregon.

APPENDIX A

Randomly Selected Spawning Surveys, 2002

Seg- Subasin Reach ID Reach Final Status Miles Spawning ment Density

Astoria Population Complex

Main Stem 30015.00 1 Cullaby Slough Zero Main Stem 30031.00 1 Abercrombie Creek Denied Main Stem 30038.00 2 Heckard Creek Zero 0.50 Main Stem 30048.00 1 Klickitot Creek Surveyed 0.20 0 Main Stem 30052.00 1 Loowit Creek Surveyed 0.99 7.1 Main Stem 30055.70 1 Lewis and Clark River Inaccessible Main Stem 30059.00 2 Lewis and Clark River Surveyed 1.70 0 Main Stem 30059.60 1 Lewis and Clark River Surveyed 1.20 0 Main Stem 30062.00 1 Crosel Creek Surveyed 1.07 1.9 Walluski River 30065.00 1 L Wallooskie River Zero Walluski River 30066.00 4 Wallooskie River Zero Walluski River 30068.00 2 Wallooskie River Surveyed 1.50 0.7 Klaskanine River 30080.70 2 Klaskanine River Inaccessible Klaskanine River 30081.70 1 Klaskanine River,N. Fk. Surveyed 1.20 56.7 Klaskanine River 30086.30 1 Klaskanine River,S. Fk. Surveyed 0.80 121.3 Klaskanine River 30086.30 2 Klaskanine River,S. Fk. Surveyed 1.60 261.9 John Day River 30116.70 3 John Day River Zero Mary’s Creek 30122.00 2 Mary’s Creek Zero Main Stem 30125.00 2 Bear Creek Surveyed 1.00 28 Main Stem 30126.00 2 Little Bear Creek Surveyed 1.10 0 Main Stem 30129.00 1 Bear Creek Zero Ferris Creek 30139.00 3 Ferris Creek Zero Main Stem 30171.00 2 Little Creek Surveyed 0.28 7.1 Main Stem 30172.00 2 Big Creek Surveyed 1.19 79 Main Stem 30172.00 3 Big Creek Surveyed 1.11 141.4 Main Stem 30192.00 2 Davis Creek Zero Main Stem 30197.00 1 Big Noise Creek Surveyed 0.99 1.0

Clatskanie Population Complex

Main Stem 30235.00 2 Hunt Creek Surveyed 0.10 50 Main Stem 30239.00 2 Plympton Creek Surveyed 1.00 13 Main Stem 30247.00 1 Olsen Creek Surveyed 0.67 1.5 Main Stem 30251.00 1 Eilertson Creek Surveyed 0.41 0 Main Stem 30261.00 2 Graham Creek Surveyed 0.85 8.2

Appendix A. Continued.

Seg- Subasin Reach ID Reach Final Status Miles Spawning ment Density Main Stem 30280.00 2 Conyers Creek Surveyed 0.90 0 Main Stem 30286.00 4 Perkins Creek Zero Main Stem 30286.00 2 Perkins Creek Surveyed 1.00 0 Main Stem 30297.00 1 Adam Creek ( Page Creek) Surveyedg 1.10 0 Main Stem 30299.00 1 Clatskanie River, N. Fk. Surveyed 0.90 1.1 Main Stem 30301.00 2 Carcus Creek Surveyed 1.10 5.5 Main Stem 30306.00 4 Clatskanie River Surveyed 1.10 0 Main Stem 30307.00 4 Little Clatskanie River Zero Main Stem 30308.00 7 Clatskanie River Surveyed 0.91 0 Main Stem 30308.00 5 Clatskanie River Surveyed 0.90 0 Main Stem 30308.00 1 Clatskanie River Surveyed 0.84 0 Main Stem 30308.70 1 Clatskanie River, Trib. 1 Surveyed 1.01 0 Main Stem 30308.90 1 Clatskanie River Surveyed 0.32 0

Scappoose Population Complex

Beaver Creek 30333.00 1 Stewart Creek Surveyed 0.30 0 Fox Creek 30378.00 2 Fox Creek Surveyed 0.80 0 Main Stem 30651.00 1 Goble Creek Surveyed 0.69 4.3 Main Stem 30652.00 2 Goble Creek, S. Fk. Surveyed 1.17 0 Main Stem 30653.00 1 Goble Creek Surveyed 0.80 2.5 Main Stem 30653.00 1 Goble Creek Surveyed a 0.80 Main Stem 30653.50 1 Goble Creek Surveyed 1.50 0 Main Stem 30656.70 5 Tide Creek Zero b Main Stem 30656.70 2 Tide Creek Surveyed 0.75 12 Main Stem 30658.00 1 Tide Creek Zero b Main Stem 30660.00 2 Tide Creek Zero b Main Stem 30784.50 8 Jackson Creek Zero Main Stem 30789.90 1 Patterson Creek Denied Main Stem 30797.00 3 Milton Creek Surveyed 1.10 1.8 Milton Creek 30797.50 1 Milton Creek Surveyed 0.90 5.6 Milton Creek 30800.00 3 CoxCreek Surveyed 0.99 7.1 Milton Creek 30801.00 1 Milton Creek Surveyed 0.96 0 Milton Creek 30803.00 1 Milton Creek Inaccessible c 1.06 Milton Creek 30807.00 1 Milton Creek Surveyed 1.10 5.5 Milton Creek 30807.00 2 Milton Creek Surveyed 0.98 1 Milton Creek 30809.00 2 Milton Creek Surveyed 1.00 0 S. Scappoose Cr. 30823.00 3 S. Scappoose Creek Surveyed 1.15 10.4 S. Scappoose Cr. 30825.50 1 S. Scappoose Creek Surveyed 1.10 28.2 S. Scappoose Cr. 30828.00 1 Lazy Creek Surveyed 0.75 0

Appendix A. Continued.

Seg- Subasin Reach ID Reach Final Status Miles Spawning ment Density S. Scappoose Cr 30829.80 1 S. Scappoose Creek Surveyed 1.20 10 N. Scappoose Cr. 30830.00 2 N. Scappoose Creek Surveyed 1.10 9.1 N. Scappoose Cr. 30832.70 1 N. Scappoose Creek Discard 0.84 N. Scappoose Cr. 30834.00 1 N. Scappoose Creek Discard

Clackamas Population Complex

Johnson Creek 30857.00 1 Crystal Springs Creek Surveyed 0.99 2 Johnson Creek 30858.00 3 Johnson Creek Discard 0.96 Johnson Creek 30858.00 1 Johnson Creek Discard d 1.16 Johnson Creek 30858.00 8 Johnson Creek Surveyed 1.10 0 Johnson Creek 30858.30 1 Kelly Creek Inaccessible Johnson Creek 30858.70 2 Johnson Creek Surveyed 1.05 0 Johnson Creek 30858.70 4 Johnson Creek Surveyed 1.02 0 Main stem 30860.00 2 Kellogg Creek Denied Main stem 30861.70 1 Mt. Scott Creek Discard e 1.00 Clear Creek 30870.00 2 Clear Creek Denied 1.40 Clear Creek 30872.00 3 Clear Creek Surveyed 1.15 5.2 Clear Creek 30873.50 1 Little Clear Creek (Soap) Surveyed 0.90 0 Clear Creek 30874.00 2 Mosier Creek (Trestle) Surveyed 0.80 00 Clear Creek 30875.30 6 Clear Creek Surveyed 1.50 15.3 Clear Creek 30875.30 2 Clear Creek Surveyed 1.50 14.7 Clear Creek 30878.00 1 Clear Creek Surveyed 0.90 6.7 Clear Creek 30880.00 1 Clear Creek Surveyed 1.10 10.9 Main stem 30885.00 1 Richardson Creek Surveyed 1.40 1.4 Main stem 30889.00 1 Deep Creek Surveyed 0.90 14.4 Main stem 30892.00 2 Deep Creek, N. Fk. Surveyed 0.80 20 Main stem 30894.00 1 Deep Creek,N. Fk. Denied Main stem 30895.30 2 Deep Creek, Trib. A Denied Main stem 30896.00 2 Tickle Creek Surveyed 1.60 31.9 Main stem 30900.00 3 Tickle Creek Denied 0.53 Main stem 30900.00 2 Tickle Creek Denied Main stem 30901.00 1 Deep Creek Surveyed 1.50 74.7 Main stem 30903.00 2 Goose Creek Surveyed 1.00 0 Eagle Creek 30907.00 3 Eagle Creek Surveyed 0.90 22.2 Eagle Creek 30907.00 5 Eagle Creek Surveyed 0.50 192 Eagle Creek 30911.00 1 Suter Creek Surveyed 1.20 0 Eagle Creek 30914.00 1 Eagle Creek, N. Fk. Surveyed 1.00 22 Eagle Creek 30919.00 2 Trout Creek Surveyed 1.10 0 Eagle Creek 30920.00 1 Eagle Creek, N. Fk Surveyed 1.50 0

Appendix A. Continued.

Seg- Subasin Reach ID Reach Final Status Miles Spawning ment Density Eagle Creek 30922.00 2 Delph Creek Surveyed 1.30 0 Eagle Creek 30923.00 4 Eagle Creek Dropped f 1.10 Eagle Creek 30923.00 2 Eagle Creek Surveyed 0.80 227.5 Main Stem 31196.00 2 Abernathy Creek Zero Main Stem 31199.50 1 Potter Creek Surveyed 1.05 0 Main Stem 31200.00 2 Abernathy Creek Denied Main Stem 31200.50 1 Abernathy Creek Surveyed 1.16 0

Sandy Population Complex

Main Stem 33395.70 1 Beaver Creek Surveyed 0.66 0 Main Stem 33407.00 2 Gordon Creek Surveyed 1.10 39.1 Main Stem 33415.00 1 Gordon Creek Surveyed 1.44 0 Main Stem 33419.00 1 Trout Creek Surveyed 0.20 0 Main Stem 33474.00 1 Cedar Creek Discard f 0.56

Bonneville Population Complex

Bridal Veil Creek 33595.00 1 Bridal Veil Creek Surveyed 0.20 30 Oneonta Creek 33613.30 1 Horsetail Creek Surveyed 0.30 110 Eagle Creek 33632.00 1 Eagle Creek No AUC f 0.73 Eagle Creek 33635.00 1 Ruckel Creek Surveyed 0.10 50 Viento Creek 33685.00 1 Viento Creek Surveyed 0.39 271.8 a Segment was randomly selected twice. b Point located above barrier falls. c Deep pools and blackberries render survey inaccessible. d Area considered unsafe for surveyors. e In-stream septic issues. f Dropped because of adjacency to hatchery.