# Presentation: 898853

## Coho Salmon (Oncorhynchus kisutch) Return to Pine Gulch Creek, Marin County, California 

_*Watershed History*_
- From the late 1800s to the mid 1900s, twenty small farms, many of them dairies, operated adjacent to Pine Gulch Creek.  Historic uses included flood irrigation, intensive livestock agriculture, logging, minor development, and mining.  A significant shift in land use began in the 1960s with the establishment of Point Reyes National Seashore (PRNS), and later Golden Gate National Recreation Area (GGNRA). Approximately 85% of the watershed is now included within NPS boundaries  These lands were acquired by the NPS between 1965 and 1980. Most agricultural operations on federal lands within the watershed have been phased out.
- Water use within Pine Gulch Creek has evolved from in-stream permanent and seasonal dams in the mid to late 1970s, to the current condition of no diversion dams within the watershed.  The most significant dam was proposed in the late 1970’s when the Bolinas Community Public Utilities District applied to construct a 35 foot high dam to create an on-stream reservoir.
- At present, five commercial operations (four organic farms and one nursery) derive their water from surface flows of Pine Gulch Creek.  A project to address water withdrawal and diversion impacts of the three most upstream commercial operations is currently in progress.
_*Pine Gulch Creek Discharge*_
- Monthly watershed production estimates have been determined by calculating water volume based on the average daily flow reported by the USGS (June 1967 – September 1970), and the NPS (May 1998 - present).  The average runoff for the watershed based on these seven years of monitoring is estimated at 9,300 acre-feet/year.  The calculated gauge watershed area is 7.5 mi2.  The data show significant seasonal and annual variability in streamflow.  The monitored range is extreme, from 2,848 acre-feet of water in WY2001 to 15,748 acre-feet in WY1998.  Approximately 75% of the rainfall and runoff occurs during the winter season (December 15 through March 31).

**Discussion                              **
- Juvenile coho salmon population estimates in Pine Gulch Creek for 2002 were twice those estimated in 2001. Although coho densities in individual pools were similar or only slightly higher in 2002, the distribution of salmon extended farther upstream with a normal distribution pattern throughout the mainstem.  In both years the downstream limit of coho distribution was within 200 meters of tidal influence.

**References**
- Brown, G.G. and B. J. Ketcham. 2002.  Documentation of Coho Salmon in Pine Gulch Creek, Marin County, CA.  Coho Salmon and Steelhead Trout Restoration Project. PORE-NR-WR-02/02. 12 pp. plus appendices.
- California Department of Fish and Game.  1968.  Field notes from Bruce Thompson and Jim Michaels – July 1968.
- Dolloff, C.A., D.G. Hankin, and G.H. Reeves.  1993.  Basinwide estimation of habitat and fish populations in streams.  Gen. Tech. Rept. SE-83.  USDA Forest Service, Southeastern Forest Experiment Station, Asheville, NC. 25 p.
- Sandercock, F.K.  1991.  Life history of coho salmon (Oncorhynchus kisutch).  Pages 395-446.  In: C. Groot and L. Margolis, eds.  Pacific salmon life histories.  UBC Press, Vancouver, British Columbia.
- VanDeventer, J.S. and W.S. Platts.  1989.  Microcomputer software system for generating population statistics from electrofishing data: users guide for Microfish 3.0.  Gen. Tech. Rept. INT-254.  USDA Forest Service, Intermountain Forest and Range Experiment Station, Ogden, UT.  29 p.

_**Coho juvenile population estimate**_
_*Habitat Survey*_
- A total of 632 habitat units were identified (285 pool, 93 flatwater, and 254 riffle units). Overall habitat composition (45 % pools, 15% flatwater, and 40% riffle) is similar to 2001.

**Results**_**          **_
***Adult Spawner Surveys***
- In the past three winters of spawner surveys, CSRP staff have observed adult coho salmon within the watershed.  This includes a single female carcass found at km 4.1 during winter 2000-2001, and a spawning pair that was observed on a redd at km 6.7 in winter 2001-2002.  In winter 2002-2003, the PLD index for Pine Gulch was 2, representing the 2 carcasses seen during the Jan. 17, 2003 survey which covered 6.3 km of stream. One redd was positively identified during the Jan. 6, 2003 survey at km 5.1.
***Outmigrant smolt trap***
- The outmigrant smolt trap was installed on March 23, 2002, although it was not fully operational until March 28.  The trap operated through May 29 for a total of 62 trapping days.  Low numbers of fry were trapped because of overflow through the upper screen weir.

**Methods**_**   **_
***Adult Spawner Surveys***
- Teams of  CSRP staff and volunteers walk upstream and along the banks, recording observations of live fish, carcasses and new redds with reference to permanent tags that mark every 100m of stream length. Observers document the species, sex, and estimated length of live fish.  The fork lengths of carcasses are measured and tissue and scale samples collected.  Redds are measured and marked with flagging.
***Outmigrant Smolt Trap***
- Outmigrant smolt pipe traps used by the CSRP are designed to minimize impingement under high flows and in-trap predation of fry by larger juvenile salmonids and other fish. CSRP outmigrant traps operate by impounding water behind a weir constructed of 13 mm square-mesh metal screen, fence posts, rocks, and sand bags that span the entire width of the stream.
- The trap operates 24 hours per day, flow permitting, and is checked daily.  Monitoring focuses primarily on salmonid smolts, parr, and fry but the numbers and lengths of all captured fish are recorded. A Hobo temperature logger is deployed and left in the trap box for the duration of operation.  All 1+ salmonids are anesthetized with carbon dioxide. Fish are weighed to the nearest 0.1 g and their fork length is measured to the nearest millimeter.  Anesthetized fish are allowed to recover fully in an aerated “recovery bucket” before release.
***Data Analysis***
- Survey data are entered and stored in a Microsoft Access database.  Data are then exported to Microsoft Excel for processing and analysis.  All calculations and population estimates are made using methods outlined in Dollof et al (1993).
***Genetic Analysis***
- Genetic clips have been collected for analysis by the NMFS Genetics lab in Santa Cruz California.  Sample collection follows NOAA-Fisheries protocol.

_**Abstract                                                                                  **_**	**
- Pine Gulch Creek, a 19.8 km2 watershed located in coastal Marin County, California, is the primary freshwater drainage to Bolinas Lagoon.  In 2001, the National Park Service (NPS) CSRP documented the return of coho salmon (*Oncorhynchus kisutch*) to the watershed. Biologists from the California Department of Fish and Game last identified coho salmon in the watershed in 1968 (CDFG 1968).  NPS monitoring has documented the return of three year classes to the watershed. This report includes monitoring results from adult spawner surveys, outmigrant smolt trapping, and a modified Hankin Reeves coho juvenile population estimate for this newly returned population.  Beginning in winter 2000-2001, coho salmon spawners have been observed in low numbers (<5 per year) within the watershed.  Results of modified Hankin-Reeves surveys, conducted during the past two Septembers, yielded estimates of 538 ( 349) juvenile coho salmon in 2001 and 1205 ( 337) juvenile coho salmon in 2002.  The 2002 survey results indicate higher abundance and wider distribution of coho than during the 2001 survey.  In response to juvenile presence in 2001, a smolt trap was operated in the spring of 2002 capturing 249 coho smolts.  Collected tissue samples have been submitted to the NOAA-Fisheries Genetics Laboratory in Santa Cruz, CA.  Preliminary results indicate that coho salmon observed in summer 2001 had a strong genetic affinity to coho salmon from the Redwood Creek watershed 6 miles south, also in Marin County. This points to natural recolonization through strays. The NPS plans to continue fisheries monitoring on an annual basis in order to track the status and trends of coho as they repopulate the watershed. Recolonization of a watershed from which coho had presumably been extirpated represents a significant gain for California’s embattled coho salmon.

**Significance**
- Based on preliminary results, genetic samples collected from juveniles in summer 2001 display an affinity to coho salmon from the Redwood Creek watershed.  This points to natural recolonization through strays.  Continued monitoring and sample collection will allow for further genetic analysis of family structure within the year classes.
- Regardless, the recolonization of a watershed from which coho had presumably been extirpated represents a significant gain for California’s embattled coho salmon.

**	****Acknowledgements**
- Project monitoring is conducted under ESA  Section 10 Permit 1046, issued to Point Reyes National Seashore and Golden Gate National Recreation Area.  Many thanks to field staff that have been integral to this monitoring: Jesse Wechsler, David Press, Jefrey Parr, Jim Whitlock, Jessica Scheeter, Odessa Wolff, and Tracie Rexer.  Darren Fong, Aquatic Ecologist at Golden Gate National Recreation Area, assisted with both field surveys and technical review.  Project monitoring has been supported through the San Francisco Area Network Inventory and Monitoring Program and the California Department of Fish and Game.

- In the 2001 monitoring report (Brown and Ketcham 2001), several theories were identified to explain the recent occurrence of three coho year classes in Pine Gulch after so many years of apparent absence.  Potential scenarios included relict year classes, planting of coho, and natural strays.
- While there have been some unconfirmed anecdotal sightings of coho over the years (winter of 1993-94 and 1996-97) it seems unlikely that the numerous surveys conducted by NPS since 1997 would have missed any relict coho populations.  However, one or more year classes could have survived in Pine Gulch Creek at levels too low for detection, and started to rebound.. Genetic analysis in this case would likely show less relatedness between the Pine Gulch coho and those from adjacent watersheds.
- Planted coho were identified as one potential repopulation scenario. The most likely relocation scenario would involve transfer of fish from Olema Creek to Pine Gulch Creek.  The presence of three year classes indicates that this is not a likely scenario.
- Preliminary results from genetic analysis by the NOAA – Fisheries Lab show that the juveniles captured in summer 2001 have a strong genetic affinity to coho salmon from Redwood Creek (Garza personal communication).  The mouth of Redwood Creek is within 6 miles of Bolinas Lagoon and Pine Gulch Creek.  Genetic data support the theory that strays from Redwood Creek could have made their way up Pine Gulch to spawn. Based on ocean bathymetry and currents, it is reasonable to assume that coho salmon from the Redwood Creek watershed could easily stray to Bolinas Lagoon and Pine Gulch Creek.  Within west Marin County, the 2000-01 and 2001-02 coho spawning runs were the strongest in several years. Considering the strong year class, straying is a likely repopulation scenario in Pine Gulch Creek.
- Tissue samples from spawner carcasses and juvenile coho, captured during electrofishing, and smolt trapping are undergoing additional genetic analysis that may indicate the degree of relatedness among the coho year classes in Pine Gulch Creek and coho from adjacent watersheds.  It is important that this is documented to determine whether these returning individuals are part of a population or an occurrence.
- Along with land acquisition and restoration efforts within NPS lands, cooperative resource protection work with private landowners in the Pine Gulch Creek watershed will continue.  The NPS plans to continue fisheries monitoring on an annual basis in order to track the status and trends of coho as they repopulate the watershed.

**Update**
- In March, 2003 a downstream outmigrant pipe trap was installed in Pine Gulch Creek. As of mid-April over 258 coho smolts have been captured.

***Coho juvenile population estimate***
- In 2002, CSRP staff conducted a modified Hankin Reeves (Dollof et.al. 1993) survey to estimate juvenile coho salmon population.  This coho survey covered approximately 8.4 km of the Pine Gulch mainstem beginning at km 0.3, the top of the dredge pool on Marin County Open Space District land (MCOSD), and continuing upstream to km 8.7.  CSRP staff habitat-typed the survey area and conducted snorkel counts in a subset of the pool units. A 250-meter section between km 7.2 and 7.5 was not surveyed because of limited access and habitat.
_*Habitat Typing*_
- Proceeding upstream on Pine Gulch Creek, CSRP staff numbered, classified, measured the length, and estimated the average width of each habitat unit. Units were classified as pool (scour pool, backwater pool, plunge pool, or mid-channel pool), flatwater, or riffle. Every fifth pool unit was flagged for snorkeling and several pool widths were measured in order to calibrate the estimated width.
_*Snorkel Counts*_
- CSRP staff sampled each of the flagged pools with a single pass snorkel count, using a dive light to search under vegetation, woody debris, and undercut banks. Only coho were counted but the presence of steelhead and non-salmonid fish were noted.  In addition, cover, habitat complexity, and general survey conditions were recorded. Calibration for the snorkel surveys was conducted using results from pools within each index reach that had been sampled two to six weeks prior to the snorkel survey.  All of the index pools were snorkeled and the electrofishing results used to calibrate the snorkel counts.

_*Snorkel counts*_
- CSRP staff dove 64 of the 285 pools, and counted a total of 239 coho in 39 of the pools. Seventeen of the 64 pools had been electrofished in the previous month.  *Microfish* population estimates for the electrofished pools were used to calibrate the snorkel counts. The calibration ratio used for this analysis is 1.1321.
- Coho densities (by both pool length and calibrated surface area), population estimate, and 95% confidence interval were calculated for the coho survey area as a whole.  Coho densities from snorkeled pools where coho were present ranged from 0.014 to 0.451 coho/m2, compared to 0.017 to 0.358 coho/m2 in 2001 (based on calibrated surface area snorkel counts).  The 2002 coho salmon juvenile population estimate is 1,205  337, more than twice the 2001 estimate.
_*Spatial Distribution of Coho Salmon *_

- The trap results are presented by species and week.  The trap captured a total of 249 coho smolts.  Coho smolts were observed beginning March 29 through May 28. Most of the coho smolts were captured during weeks 7 and 8 of trap operation.  No coho fry were captured. Also captured were 240 steelhead fry (including 11 mortalities), 7 steelhead smolts, 20 steelhead presmolts, and 27 steelhead parr.  Most of the steelhead young of year were captured during week week 6.

- Correlation between visually estimated and measured surface area of 78 pools was adequate (R2=0.91).  A calibration ratio of 1.10 was used to correct the estimated surface area of all units

- Correlation between electrofishing and snorkel counts was adequate (R2=0.86) and a calibration ratio of 1.1321 was used to correct the snorkel counts for all pools

- The 2002 coho salmon distribution pattern (left) was normal compared to the bimodal or clustered distribution found in 2001 (below).  The observed gap in the 2001 distribution (from approximately km 4.5 to 5.7), coincided with an area affected by cattle grazing in an unfenced pasture adjacent to the creek from km 5.0 to 5.7. This same section had the highest numbers of juvenile coho in 2002.  In addition, an adult female coho on a redd, representing a third year class, was seen in this area at km 5.0 in January 2003.

- The downstream limit of coho distribution was similar in both years, but appeared to extend farther upstream in 2002.  The 2002 survey was longer than that completed in 2001 and coho were seen from km 0.4 to 7.8. Six pools in McCurdy Creek (the largest eastern tributary of Pine Gulch Creek) were snorkeled.  Two of the five pools below the State Route One culvert contained a total of 13 coho, and the single isolated pool sampled in the mostly dry section above the culvert contained steelhead but no coho.  The State Route 1 culvert is recognized as an impediment to fish passage, and the presence of coho salmon in the tributary is significant.

**National Park Service**
**Point Reyes Reyes National Seashore**

**Coho Salmon (*****Oncorhynchus kisutch*****) Return to Pine Gulch Creek, Marin County, California**** **
**Coho Salmon & Steelhead Trout Restoration Project (CSRP)**
**Brannon Ketcham, Hydrologist, & Greg Brown, Biological Technician **
- Point Reyes National Seashore, Point Reyes Station, CA  94956
- contact: brannon_ketcham@nps.gov