DATA REPORT€¦ · Appendix 2: A Standardized Approach for Habitat Assessments and Visual Encounter Surveys for the Foothill Yellow-Legged Frog (Rana boylii) (Seltenrich and Pool

DATA REPORT

RESULTS OF 2004 SURVEYS AND MONITORING FOR FOOTHILL YELLOW-LEGGED FROG (Rana boylii) WITHIN THE

ROCK CREEK-CRESTA PROJECT AREA, NORTH FORK FEATHER RIVER, AND 2002-2004 RECREATION AND PULSE

FLOW BIOLOGICAL EVALUATION SUMMARY

Prepared for:

PACIFIC GAS & ELECTRIC COMPANY TECHNICAL AND ECOLOGICAL SERVICES

3400 CROW CANYON ROAD SAN RAMON, CALIFORNIA 94583

Prepared by:

GARCIA AND ASSOCIATES 1 SAUNDERS AVENUE

SAN ANSELMO, CALIFORNIA 94960

July 2005

JOB 332/80

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Rock Creek-Cresta Project, FERC No. 1962 Recreation and Pulse Flow Biological Evaluation Study

© 2005, Pacific Gas and Electric Company

TABLE OF CONTENTS

1.0 INTRODUCTION....................................................................................................... 1

1.1 FYLF STATUS, DISTRIBUTION AND CURRENT THREATS TO POPULATIONS......................................................................................................................................... 1

2.0 METHODS .................................................................................................................. 5

2.1 HABITAT ASSESSMENTS...................................................................................... 5 2.2 VISUAL ENCOUNTER SURVEYS.......................................................................... 5 2.3 DETERMINATION OF ONSET AND DURATION OF FYLF BREEDING AND RATE OF DEVELOPMENT............... 7 2.4 PULSE FLOW AND RECREATIONAL FLOW MONITORING PROTOCOL AND SCHEDULE..................................................................................................................... 8 2.5 UNDERWATER VIDEO MONITORING................................................................. 9 2.6 REACH WIDE SURVEY — ROCK CREEK REACH .......................................... 11 2.7 DETRITUS STUDY................................................................................................ 12 2.8 FYLF FUNGAL EGG MASS TESTING .............................................................. 13 2.9 GARTER SNAKE PREDATION STUDY............................................................... 14 2.10 2003 TADPOLE ATTRITION STUDY .............................................................. 14

3.0 RESULTS .................................................................................................................. 15

3.1 HABITAT ASSESSMENTS.................................................................................... 15 3.1.1 Habitat Assessments- Cresta Reach ................................................................ 16 3.1.2 Habitat Assessments- Rock Creek Reach......................................................... 22

3.2 VISUAL ENCOUNTER SURVEY RESULTS ........................................................ 25 3.2.1 VES Results by FYLF Life Stage...................................................................... 25 3.2.2 Site-specific Results ......................................................................................... 47

3.3 ONSET AND DURATION OF FYLF BREEDING AND EGG MASS DEVELOPMENT........................................................................................................... 56 3.4 PULSE FLOW AND RECREATIONAL FLOW MONITORING ............................ 57 3.5 UNDERWATER VIDEO MONITORING............................................................... 61 3.6 REACH WIDE SURVEY - ROCK CREEK REACH ............................................. 64 3.7 DETRITUS STUDY................................................................................................ 66 3.8 FYLF EGG MASS TESTING............................................................................... 70 3.9 GARTER SNAKE PREDATION STUDY............................................................... 71 3.10 2003 TADPOLE ATTRITION STUDY .............................................................. 72

4.0 DISCUSSION ............................................................................................................ 75

4.1 EGG MASSES........................................................................................................ 75

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4.2 DETACHED EGG MASSES .................................................................................. 76 4.3 FUNGUS................................................................................................................. 76 4.4 SNORKELING........................................................................................................ 76 4.5 UNDERWATER VIDEO MONITORING............................................................... 77 4.6 PREDATION .......................................................................................................... 78 4.7 FLOW EFFECTS ON SMALL TADPOLES – TADPOLE ATTRITION................. 78 4.8 FLOW EFFECTS ON LARGE TADPOLES............................................................ 79 4.9 DETRITUS, ALGAE, AND MACROINVERTEBRATES ....................................... 79 4.10 SEARCH AND RESCUE OPERATIONS ............................................................. 79 4.11 STRANDING........................................................................................................ 80 4.12 FLOW EFFECTS ON JUVENILES....................................................................... 80 4.13 JUVENILE RECRUITMENT ................................................................................ 81 4.14 ADULT MALES IN A FRAGMENTED POPULATION....................................... 81 4.15 MINIMUM INSTREAM FLOW REQUIREMENTS, SPRING FLOW REGULATION, AND THE ONSET OF BREEDING..................................................... 82 4.16 RECREATIONAL FLOW EFFECTS AT STAFF GAUGES.................................... 83

5.0 SUMMARY ............................................................................................................... 83

6.0 LITERATURE CITED ............................................................................................ 85

FIGURES: Figure 1.0-1 FYLF survey and monitoring locations in the Cresta Reach. ........................ 3 Figure 1.0-2 FYLF survey and monitoring locations in the Rock Creek Reach Project

area.............................................................................................................................. 4 Figure 2.3-1. Gosner staging table used to determine FYLF developmental stage (from

Duellman and Trueb, 1986). ....................................................................................... 7 Figure 3.2-1. FYLF egg mass distribution and frequency on the Cresta Reach, North Fork

Feather River, 2002-2004. ........................................................................................ 26 Figure 3.2-2. Distance from shore and corresponding depths of egg mass and stream

bottom for 31 FYLF egg masses observed in the Cresta Reach, NFFR, 2004. ........ 28 Figure 3.2-3. Distance from shore and corresponding depths of egg mass and stream

bottom for 66 FYLF egg masses observed in the Cresta Reach, 2002-2004............ 28 Figure 3.2-4. Depth and distance to shore for tadpole groups in July (N = 125) and

August (N = 37) 2002-2004 (pooled) as recorded during VES monitoring on the Cresta Reach, NFFR. ................................................................................................ 33

Figure 3.2-5. Mean number of tadpole observations at each subsite prior to and following the July 2004 recreational flow, Cresta Reach, NFFR.............................................. 36

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Figure 3.2-6. Tadpole mortality at Subsite 1a found in shallow water the day following the search and rescue operation associated with the 24 July 2004 recreational flow.................................................................................................................................... 37

Figure 3.2-7. Injured FYLF tadpole found 26 July 2004 at Subsite 6b 48 hours following the 24 July recreational flow..................................................................................... 37

Figure 3.2-8. Temporal distribution of adult and juvenile FYLF during 2004 VES in the Cresta Reach, NFFR. ................................................................................................ 41

Figure 3.2-9. Mean number of adult frogs observed per survey during recreational flow monitoring on the Cresta Reach 2002-2004 – May through October....................... 45

Figure 3.2-10. Mean number of adult frogs observed per survey during recreational flow monitoring on the Cresta Reach 2002-2004 – May and June only........................... 45

Figure 3.2-11. Mean number of juvenile FYLF observed per survey during VES on the Cresta Reach around recreational flows in September and October 2002, 2003, and 2004........................................................................................................................... 47

Figure 3.3-1. Time of estimated FYLF egg mass occurrence on the Cresta Reach, NFFR, 2002-2004. .............................................................................................................. 57

Figure 3.5-1. Signal crayfish feeding on egg mass “A” at Subsite 9e on 14 June 2004 at 1811 hrs..................................................................................................................... 63

Figure 3.7-1. Before (top) and after (bottom) recreational flow photos at quadrat sample location in fast flow portion of Subsite 1a. ............................................................... 68

Figure 3.7-2. Before (top) and after (bottom) recreational flow photos at quadrat sample location in slow flow portion of Subsite 1a. ............................................................. 69

Figure 3.8-1. Squash preparation of FYLF egg mass infected with Saprolegnia............ 70 Figure 3.9-1. Thamnophis couchii regurgitating 23 FYLF tadpoles (Gosner stage 25)

near egg mass “D” at Site 9e, 19 June 2003 ............................................................. 71 Figure 3.10-1. Plot of 16 counts of tadpole groups on the Cresta and Poe Reaches of the

NFFR......................................................................................................................... 73 Figure 3.10-2 Comparison of tadpole attrition rate on the Cresta Reach and Poe Reach,

NFFR......................................................................................................................... 73 TABLES: Table 2.3-1 Comparison of Gosner’s (1960) anuran stages of development and field

developmental stages for egg masses used during 2003-2004 surveys on the Rock Creek-Cresta Project area, NFFR. .............................................................................. 8

Table 2.4-1. 2004 Flow Schedule for the Rock Creek and Cresta Reaches, NFFR. .......... 9 Table 3.1-1. Subsites within the Rock Creek-Cresta Project Area for which habitat

assessments were conducted from 2001-2004.......................................................... 15 Table 3.2-1. Summary of FYLF oviposition site habitat parameters in the Cresta Reach,

2004 and 2002-2004. ................................................................................................ 27 Table 3.2-2. Summary of habitat characteristics associated with FYLF egg masses in the

Cresta Reach, NFFR in 2004 and from 2002-2004.. ................................................ 30 Table 3.2-3. Summary of 2003-2004 egg masses discovered using snorkeling versus

conventional wading techniques. .............................................................................. 31

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Table 3.2-4. Characteristics of FYLF tadpoles and habitat for tadpole groups observed on the Cresta Reach, NFFR from 2002-2004.. .............................................................. 33

Table 3.2-4. Characteristics of FYLF tadpoles and habitat for tadpole groups observed on the Cresta Reach, NFFR from 2002-2004.. .............................................................. 34

Table 3.2-5. Tadpole observations associated with the July 2004 recreational flow. ...... 35 Table 3.2-6. Tadpole observations at each subsite associated with the August 2004

recreational flow. ...................................................................................................... 38 Table 3.2-7. Pooled data comparisons of tadpole numbers found during VES on the

Cresta Reach before and after recreational flows during 2002-2004. ...................... 39 Table 3.2-8. Temporal distribution of adult and juvenile FYLF observations by month

during 2004 surveys in the Cresta Reach, NFFR. ................................................... 40 Table 3.2-9. Distribution of adult and juvenile FYLF observed by subsite in the Cresta

Reach, NFFR in 2004. .............................................................................................. 42 Table 3.2-9. Distribution of adult and juvenile FYLF observed by subsite in the Cresta

Reach, NFFR in 2004. .............................................................................................. 42 Table 3.2-10. Mean Snout-Vent Length (SVL) for adult and juvenile FYLF observed in

Cresta Reach, NFFR 2004. ....................................................................................... 42 Table 3.2-11. Pooled data comparisons of juvenile numbers found during VES on the

Cresta Reach before and after recreational flows during 2002-2004. ...................... 44 Table 3.2-12. Summary of juvenile recruitment numbers from all survey sites on the

Cresta Reach 2002-2004, and between-year comparisons at four subsites (1a, 6b, 9a, 9e) that were monitored each year 2002-2004.......................................................... 46

Table 3.2-13. Visual Encounter Survey Results for Site 1, Shady Rest Area, Rock Creek-Cresta Project Area. .................................................................................................. 49

Table 3.2-14. Visual Encounter Survey Results for Site 6, Cresta Powerhouse Area, Rock Creek-Cresta Project Area. ....................................................................................... 51

Table 3.2-15. Visual Encounter Survey Results for Site 9, Cedar Creek Area, Rock Creek-Cresta Project Area. ....................................................................................... 54

Table 3.4-1. Annual values and overall pooled means during recreational flows for the three measured hydrological parameters at 25 staff gauges installed from 2002-2004 on the Cresta Reach .................................................................................................. 59

Table 3.6-1. Summary of surveys conducted on tributaries within the Rock Creek Reach, North Fork Feather River.......................................................................................... 64

Table 3.7-1. Mean cover values for detritus and algae in selected sample plots (0.1 m quadrats) within tadpole habitats at seven subsites on the Cresta Reach before and after the July 2004 recreational flow.

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....................................................................... 67Table 3.9-1. Sierra garter snake (Thamnophis couchii) stomach contents containing FYLF

recorded on the NFFR, 2003-2004. .......................................................................... 71 Table 3.10-1. Count data used for statistical analysis of tadpole attrition........................ 74

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APPENDICES: (Provided in a separate volume) Appendix 1: Foothill Yellow-legged Frog Life History and Habitat Preferences Appendix 2: A Standardized Approach for Habitat Assessments and Visual Encounter

Surveys for the Foothill Yellow-Legged Frog (Rana boylii) (Seltenrich and Pool 2002)

Appendix 3: Habitat Assessment Forms and Site Sketch Maps Appendix 4: Aerial Photographs of Survey Sites and Transect Locations Appendix 5: Representative Site, Microhabitat, and FYLF Photographs, Photo Log Appendix 6: Visual Encounter Survey Data Forms Appendix 7: Underwater Video Monitoring Data Forms Appendix 8: Representative Underwater Video Images Appendix 9: Rock Creek Reach-wide Data Sheets and Appended Aerial Photographs Appendix 10: Detritus Study Data Forms Appendix 11: Flow Monitoring Study Plan dated 7 March 2002 (PG&E 2002a) and

revised on 7 May 2003 (PG&E 2002b).

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1.0 INTRODUCTION Pacific Gas and Electric Company (PG&E) owns and operates the Rock Creek-Cresta Hydroelectric Project (Project) in northeastern California. The Rock Creek-Cresta Project is licensed by the Federal Energy Regulatory Commission (FERC) and is referred to as FERC No. 1962. As part of the relicensing process, a Settlement Agreement was produced that outlines the protection, mitigation, and enhancement measures recommended for the new project license. The Settlement Agreement provides for recreational streamflows and pulse flows ranging from 800 to 1600 cfs in all water-year types. The Settlement Agreement also specifies boater use triggers that will provide additional recreational streamflow releases if both the Ecological Review Committee (ERC) and the Forest Service (FS) determine, after three years of data collection and assessment, that recreational streamflow releases do not cause unacceptable adverse ecological effects. To make this determination, studies were conducted to evaluate the effects of recreational streamflows and pulse flows on amphibians, fish, and macroinvertebrates in the Cresta and Rock Creek reaches of the North Fork Feather River (NFFR). Figures 1.0-1 and 1.0-2 show the survey and monitoring locations within both reaches. In 2001, preliminary habitat assessments and visual encounter surveys for amphibians were conducted within the Project area (ECORP 2002). In 2000, PG&E biologists identified sites with amphibian habitat potential. In support of the Settlement Agreement, PG&E contracted Garcia and Associates (GANDA) to conduct surveys and monitoring for foothill yellow-legged frog (Rana boylii; FYLF) in the Rock Creek-Cresta Project area from 2002-2004. Herein, we report on results of 2004 surveys and monitoring and provide a comprehensive summary of 2002-2004 results. Results of 2002 and 2003 surveys and monitoring are provided in GANDA (2004a) and GANDA (2004b) reports.

1.1 FYLF Status, Distribution and Current Threats to Populations The FYLF is designated as a Federal Species of Concern, a Forest Service Sensitive species, and a California Species of Special Concern. FYLF occur in the Coast Ranges from the Santiam River in Oregon south to the San Gabriel River in Los Angeles County and along the west slopes of the Sierra/Cascade crest in most of central and northern California. Other isolated populations have been reported in Baja California Norte (Loomis 1965), in southern California, and at Sutter Buttes in Butte County, California (Stebbins 2003). Livezey (1963) reported a locality 8 km north of Lodi, in San Joaquin County on the floor of the Central Valley, which appears to have been a displaced frog from the foothills. The elevational range of FYLF extends from sea level to 2,042 m (~6,700 ft.) in Baja California Norte. In California, FYLF have been recorded in the Sierra as high as 1,830 m (6,000 ft.) near McKessick Peak, Plumas National Forest and 1,940 m (6,365 ft.) at Snow Mountain in Trinity County (Stebbins 2003). The highest

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elevational record from the nearby Lassen National Forest for FYLF lies at 890 m (2,920 ft.) at Deer Creek in Tehama County (Koo et al. 2004). FYLF have been recorded at locations within the Project area along the lower reaches of the NFFR and its tributaries upstream of Lake Oroville and downstream of the Cresta Dam, associated with both the Poe and Rock Creek-Cresta hydroelectric projects (ECORP 2002; GANDA 2004a, GANDA 2004b, GANDA 2004c). In Butte County near the Project area, FYLF have been recorded along the West Fork Feather River three miles southeast of Stirling City, along Little Butte Creek at Paradise Reservoir, and Little Butte Creek at Hupp Contelene Road (Koo et al. 2004). FYLF have not been observed in the Upper North Fork Feather River drainage (GANDA 2002b; Zweifel, R.G., unpublished field notes 1952; UNFFR License App. - PG&E 2002c). Other records from Plumas County include observations in the Middle Fork Feather River drainage and tributaries of the East Branch North Fork Feather River drainage (Koo and Vindum 1999), including an unverified observation near the Halstead Campground area (C. Herrala, PG&E, pers. comm., 2003). Surveys conducted on Bean Creek along the Spanish Creek drainage, east of the Project area, found adult FYLF occurring within less than one mile of mountain yellow-legged frogs (Rana muscosa; MYLF) (GANDA 2002a). The FYLF locality occurred at an elevation of 1,372 m (4,400 ft.) while the MYLF were located at 1,440 m (4,500 ft.). In the Sierra Nevada, FYLF have disappeared from an estimated 66 percent of its former range (Stebbins 2003). Non-native predators, land use conversion, pesticide use, and modification of hydrology are considered the main threats to FYLF populations (Davidson et al. 2002; Jennings and Hayes 1994). Non-native bullfrogs (Rana catesbeiana) negatively affect FYLF populations via larval competition and direct predation (Moyle 1973; Crayon 1998; Kupferberg 1997). Signal crayfish feed on FYLF eggs and tadpoles (GANDA 2004b; Rombough and Hayes, in press; Wiseman, in press, this study) and have been shown to negatively affect the species through direct predation and egg mass displacement in ponds (Nyström et al. 2001). Invasive fish, particularly centrarchids, are suspected to feed upon FYLF (Van Wagner 1996; Werschkul and Christensen 1977). Construction of dams and altered hydrological systems continue to threaten FYLF populations by reduction of breeding habitat and scouring of egg masses by untimely water releases (Lind et al. 1996; GANDA 2004a). A complete account of the life history and habitat preferences of FYLF is provided in Appendix 1.

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2.0 METHODS 2.1 Habitat Assessments Detailed habitat assessments were conducted by GANDA and PG&E biologists at each pre-determined survey site according to A Standardized Approach for Habitat Assessments and Visual Encounter Surveys for the Foothill Yellow-Legged Frog (Rana boylii) (Seltenrich and Pool 2002; Appendix 2). Site locations were chosen by PG&E biologists Craig Seltenrich and Alicia Pool and GANDA biologist Ron Jackman during ground surveys on 21 and 28 May 2002. Site selection was based on the presence of habitat features favorable for FYLF and on results of previous FYLF surveys in the Project area (ECORP 2002). The nine sites encompassed several distinct areas of potential habitat (e.g., various cobble/boulder bars, pool tail-out), therefore the sites were divided into subsites based distinct habitat changes as described in Seltenrich and Pool (2002). Aerial photographs of the subsites are provided in Appendix 4. A separate habitat assessment form was completed for several subsites within a site. In teams of two, GANDA biologists Ron Jackman, Joe Drennan, Kevin Wiseman, Karla Marlow and PG&E biologists Craig Seltenrich and Alicia Pool performed initial habitat assessments in the Project area in 2002 (Table 3.1-1; Appendix 3). Key habitat parameters recorded during habitat assessments included: amphibian habitat type (e.g., cobble/boulder bar), general river habitat type; river and bank gradient; percent aquatic and terrestrial cover; terrestrial and aquatic substrate; and margin, emergent, and submerged vegetation. Site measurements were determined using a 100-meter tape or a rangefinder. Distance to nearest tributary for each subsite was recalculated in 2004 based on field information acquired during the monitoring period. Habitat photographs were taken at all sites, usually during the habitat assessment procedure. An attempt was made to take photographs of upper (upstream), middle, and lower (downstream) portions of all sites and subsites. A complete photo log of all pictures taken at survey sites in 2004 and representative photos showing subsites is included in Appendix 5.

2.2 Visual Encounter Surveys Visual Encounter Surveys (VES) were conducted by GANDA and PG&E biologists according to A Standardized Approach for Habitat Assessments and Visual Encounter Surveys for the Foothill Yellow-Legged Frog (Rana boylii) (Seltenrich and Pool 2002; Appendix 2). Surveys were conducted during the spring, summer, and fall of 2004 by GANDA biologists Ron Jackman, Joe Drennan, Karla Marlow, Kevin Wiseman, Ian Chan, Jason Minton, Jeff Mitchell; and PG&E biologists Alicia Pool, Andrea Herman, and Mike Carbiener. The timing and number of VES was intended to document every

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life stage of FYLF (egg, larval, metamorph) and also followed the schedule of recreational flows determined prior to the field season (Table 2.4-1). Early season egg mass surveys were conducted initially to determine the onset of breeding, and to establish which subsites would be monitored as part of the recreational flow study. All sites shown in Figures 1.0-1 and 1.0-2 were surveyed at least once in the spring of 2004. Surveys were then conducted following the recreational flow schedule (Section 2.4). All VES were conducted between 0900 and 1800 hrs. Although the Survey Protocol recommends conducting surveys on warm, sunny days with little to no wind, these conditions were not consistently present, and a few surveys were conducted during less favorable conditions. All VES were conducted from the downstream end to the upstream end of the site or subsite. Polarized sunglasses and Plexiglas viewing boxes (12 in. x 18 in. x 3 in.) were used to reduce glare and increase visibility of aquatic habitats. Care was taken to minimize disturbance to frogs and aquatic habitats. The snorkeling technique was used during all egg mass VES. Surveys were usually conducted in teams of two. Occasionally surveyors worked in teams of three, or separately to cover smaller subsites. During egg mass surveys in 2003 and 2004, one biologist typically walked and waded along the shoreline while the other snorkeled alongside in edgewater areas. The pedestrian surveyor searched ahead for adult frogs along shore and searched edgewater habitats for egg masses by using a Plexiglas viewing box, and by carefully feeling under overhanging boulders and in boulder crevices. The snorkeling surveyor searched deeper waters (to ~2 m deep) and ranged out to 10 m or more from the wetted edge. Data from VES were recorded onto Visual Encounter Survey Data Sheets for each subsite surveyed. Separate data sheets were completed for egg masses, tadpoles, and juveniles and adults. Copies of all completed data sheets are provided in Appendix 6. The data parameters collected for FYLF egg masses included: location within site; attachment substrate; distance from shore; depth of egg mass and maximum stream depth; velocity; microhabitat; stream substrate; water temperature; surface velocity; egg mass shape; egg mass color; and Gosner/field stage (Section 2.3). The data parameters collected for FYLF tadpoles included: tadpole group location in site; number of tadpoles in group; distance from shore; velocity; tadpole stage and size; substrate; percent algae and detritus; water depth and Gosner/field stage. The data parameters collected for juvenile and adult FYLF included: number of frogs observed; frog location within site; sex; age; snout-vent length; habitat type; activity; percent cover of vegetation; percent shade and substrate. GANDA biologists notified PG&E personnel at the Rock Creek Powerhouse Switching Center at the start and end of each survey day when working on the NFFR.

2.3 Determination of Onset and Duration of FYLF Breeding and Rate of Development

In order to estimate the onset of FYLF breeding, the date egg masses were first observed was compared against developmental periods reported in Ashton et al. (1998) and Zweifel (1955) (27-36 days and 5-30 days, respectively). This information was further linked with information from VES egg mass data (Gosner stage, color of egg mass, etc.) to determine the approximate age of egg masses, estimate the onset of breeding, and calculate the date when hatching was complete. In 2003 and 2004, all egg masses and tadpoles were evaluated to determine their developmental stage using Gosner’s (1960) (Figure 2.3-1) descriptions, as well as a simplified field stage classification developed by biologist Wendy Roberts (Table 2.3-1).

Figure 2.3-1. Gosner staging table used to determine FYLF developmental stage (from Duellman and Trueb, 1986).

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Table 2.3-1 Comparison of Gosner’s (1960) anuran stages of development and field developmental stages for egg masses used during 2003-2004 surveys on the Rock Creek-Cresta Project area, NFFR.

Field Stage

Gosner Stages

Description

1 1-8 Embryos round, light and dark poles visible, light and dark hemispheres roughly equal in size.

2 9-13 Embryos round, mostly dark with a small light area. Distinguish from previous field stage by reduction in light hemisphere.

3 14-16 Distinctly elongate, small folds on one edge gradually become more prominent. Distinguish from previous field stage by change from round to elongate form.

4 17-20 Small tail bud gradually becomes larger. Touch an embryo at stage 18 or higher and it should twitch. Distinguish from previous field stage by distinct tail bud.

5 21-22 FYLF usually hatch at stages 20-22. At 21, cornea becomes transparent and eye is clearly distinguished. At 22, tail fin becomes transparent (might be hard to see).

2.4 Pulse Flow and Recreational Flow Monitoring Protocol and Schedule Protocols for FYLF monitoring during recreational flows were developed by PG&E biologists and summarized in a study plan dated 7 March 2002 (PG&E 2002a) and revised on 7 May 2003 (PG&E 2002b). The study plan provides the rationale and study approach associated with flow monitoring for the Project (Appendix 11). The plan was modified based on input from the ERC on 19 March 2003. These modifications included moving early season pulse flows up to January, February, or March, and restricting recreational flows until 21 days after all egg masses had hatched, and conducting only two surveys surrounding the September and October recreational flows (24 hours before and after each flow event). The basic schedule for monitoring FYLF sites in 2004 included four VES surrounding each flow event, except as stated above. Visits were conducted at 48 and 24 hours before flow events and 24 and 48 hours after each flow event. Flow events for 2004 were scheduled for the third weekend in each month from June to October (Table 2.4-1). Recreational flow events were not monitored on the Rock Creek Reach in 2004, based on results of reach-wide VES surveys conducted from 14-18 June 2004 that found no FYLF or egg masses (Section 3.6). Prior to the July flow event, staff gauges were installed in the Cresta Reach at Subsites 1a, 1d, 6b, 9a, 9b, 9d, and 9e along the shoreline wetted edge at or near known FYLF oviposition sites. The metered gauges provided a method to determine depth change, and

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estimate shore distance and velocity changes during recreational flows. Photographs (Appendix 5) were taken of each staff gauge at base flow and again during recreational flows for visual comparisons, and data were recorded on stage height (depth), surface velocity and distance of staff gauge to the new wetted edge. Surface velocity at or adjacent to staff gauges was estimated by calculating the approximate distance floating debris traveled past the staff over a two-second period and dividing by two. Table 2.4-1. 2004 Flow Schedule for the Rock Creek and Cresta Reaches, NFFR.

DATE FLOW TYPE and DURATION LOCATION June 26, 2004 a 1,600 cfs pulse and recreation flow- 6am to 6pm Cresta Reach June 27, 2004 1,600 cfs pulse and recreation flow- 6am to 6pm Rock Creek Reach July 24, 2004 1,200 cfs recreation flows- 10am to 4pm Cresta Reach July 25, 2004 1,200 cfs recreation flows- 10am to 4pm Rock Creek Reach August 28, 2004 1,000 cfs recreation flows- 10am to 4pm Cresta Reach August 29, 2004 1,000 cfs recreation flows- 10am to 4pm Rock Creek Reach September 25, 2004 1,000 cfs recreation flows- 10am to 4pm Cresta Reach September 26, 2004 1,000 cfs recreation flows- 10am to 4pm Rock Creek Reach October 23, 2004 1,000 cfs recreation flows- 10am to 4pm Cresta Reach October 24, 2004 1,000 cfs recreation flows- 10am to 4pm Rock Creek Reach

aScheduled flow was cancelled to limit potential damage to FYLF egg masses.

2.5 Underwater Video Monitoring In an effort to better understand potential disturbance to and predation on FYLF egg masses, a pilot study was initiated in 2003 utilizing an underwater video camera and standard videocassette recorder (VCR) at breeding sites in the Cresta Reach. In 2004, the recording system was modified by replacing the VCR with a digital video recorder (DVR) to improve video quality and operational logistics. The VCR limited recording to eight to ten hours on a single tape, requiring two visits per day to change the tapes, which did not allow for constant video coverage. The DVR can record constantly for several days without maintenance, depending on the parameter settings and power source. The digital video system consisted of an Aqua-vu© Underwater Infrared Video System, Z Series, connected to an Echovue 405, 4-channel - DVR - with an 80 gigabyte internal hard drive. A small television was used to display the DVR’s system menu, which was necessary to set-up the recording parameters. The DVR was powered by a 300-watt power inverter drawing from three deep cycle marine batteries. The television and Aqua-vu camera were powered directly from the deep cycle batteries. The recording parameters of the DVR were set to record continuously at “super” quality and 10 frames-per-second (fps). The DVR provided a range of fps rates from 30 fps (real-time) to three fps. Increased fps results in larger video file sizes, and reduces the duration that can be captured on the memory of the internal hard drive. Using 10 fps

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maximized the video quality, while allowing the DVR to record one camera continuously for at least three days. The DVR can accept video input from up to four cameras, and we intended to deploy two Aqua-vu cameras at two egg mass locations. In addition to diurnal recordings, the infrared lighting of the Aqua-vu camera allowed nocturnal monitoring. The DVR can be set to detect motion, which then triggers recording. We intended to determine if this feature could further reduce the quantity of memory utilized, by not recording when movement levels were low. Settings allowed a range of sensitivity levels, and we speculated that the lowest sensitivity setting may be suitable, since egg masses are constantly in motion due to river flow. If the presence of a disturbance factor, such as a crayfish, could be detected and recorded, then the quantity of repetitive videos could be reduced when the egg masses were not being disturbed. A video monitoring system with a design similar to that of 2003 (recording on video cassettes) was prepared as a backup. This system was deployed at a second site, to monitor a second egg mass (Subsite 6b), when it was confirmed that only a single egg mass could be located in the initial study area (Subsite 9e). The second video recording system used a VCR (RCA AC/DC AccuSearch videocassette recorder; Model # VR637HF). The VCR was powered by the same batteries described for the DVR system. We used 8- or 10-hour VHS videotapes, which were the longest lasting tapes readily available. The video systems were placed in plastic storage lockers positioned inconspicuously among vegetation adjacent to each monitoring site. A 120-foot long cable connected the video recorder to the camera, which was positioned in the river approximately 30-40 cm from the egg masses. After confirming accurate camera positioning, each system was left in place to operate. Following video monitoring, all video files and tapes were reviewed to record all pertinent activities that occurred during each monitoring period. For each digital video file and tape, we recorded the start and end time, counter reading (VHS tape), time and duration of each observation, and relevant details of each disturbance event, including the species present, number of individuals, and the outcome of the observation. We also recorded relevant egg mass data including depth, distance from shore, attachment substrate, orientation to flow, Gosner (1960) stage and microhabitat. All significant observations of other species (i.e., crayfish, smallmouth bass, etc.) were recorded. Common (e.g., juvenile and young-of-the-year fish) or insignificant observations (e.g., large pieces of Cladophora) that recurred frequently were not recorded. Completed video monitoring data sheets are provided in Appendix 7, and representative images captured during monitoring are provided in Appendix 8.

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Between 2 and 20 June 2004, we operated video monitoring systems at two egg mass sites. A single egg mass was monitored at each of subsites 6b and 9e on the Cresta Reach. Monitoring at Subsite 9e was recorded by DVR, and Subsite 6b was recorded on VHS tapes by a VCR. The duration of monitoring and recording at Subsite 9e was 304 hours and 29 minutes, during 17 days between 2 and 20 June. The duration of recording at Subsite 6b was 45 hours and 33 minutes, during 6 days between 7 and 19 June. This equates to a total of 23 camera-days (including partial days) logged at both sites combined. Recording was not continuous over the period due to the logistics of changing VHS tapes and powering the systems with batteries. Predators, physical disturbance, incidental wildlife observations and egg mass condition were documented during 180 hours of video taping at two sites. Representative observations were compiled, and the video file format was converted and recorded onto DVD.

2.6 Reach Wide Survey — Rock Creek Reach An early season reach-wide survey focusing on FYLF egg masses and adults was conducted in the Rock Creek Reach from 14-18 June 2004. Two teams of two or three biologists performed the survey: GANDA biologists Kevin Wiseman and Jeff Mitchell (conducting snorkeling surveys) and PG&E biologists Alicia Pool, Andrea Herman, and Mike Carbiener (conducting shoreline surveys or car shuttling). Survey crews consisting of one snorkeler and one shoreline surveyor began from the downstream end of the reach working upstream on both sides of the river. The survey area included the thirteen formally designated sites/subsites, as well as intermediate areas that had not been previously surveyed. Some small areas were determined to be unsafe to survey due to access problems and were not included in the survey area (i.e., areas “F-G” near the Rock Creek Powerhouse; Appendix 9). Appendix 9 includes aerial photographs with field notes of areas surveyed. Late season VES focusing on FYLF juveniles and adults were conducted in the Rock Creek Reach from 23-29 October 2004. Two teams of two biologists performed the late season surveys: GANDA biologists Ron Jackman and Kevin Wiseman and PG&E biologists Alicia Pool and Andrea Herman. Survey crews resurveyed the thirteen formally designated river sites/subsites and also searched eight tributaries to the Rock Creek Reach. An effort was made to survey tributaries adjacent to mainstem river sites considered to have moderate-to-good FYLF habitat. In an effort to determine if any historical records exist for FYLF in the Rock Creek Reach, we contacted Dr. Richard Zweifel in July 2004 by phone. On 28 September 2004 field notes of biologists known to have worked in the general area (R.G. Zweifel, R.C. Stebbins, H.S. Fitch, and H.I. Fisher) were searched in the Grinnell Library, Museum of Vertebrate Zoology, U.C. Berkeley by Kevin Wiseman and Karla Marlow.

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2.7 Detritus Study Background FYLF tadpoles feed on algae scraped from rocks or plants, especially epiphytic diatoms (S. Kupferberg pers. comm. in Jennings and Hayes 1994). In addition, FYLF regularly take cover in detritus, substrate interstices, and aquatic vegetation including filamentous algae (Seltenrich and Pool 2003; GANDA, field observation). In 2002 and 2003, more large tadpoles were observed during VES conducted after recreational boating flows than before recreational flows in the Cresta Reach (Section 3.2.1.2). This result may be due to the effects of these flows on the amount or distribution of detritus and algae used as cover. An examination of detrital and algal cover percentages estimated at tadpole locations in 2003 as specified in the Survey Protocol (Seltenrich and Pool, 2002) revealed that cover values for algae (mostly epiphytic) did not change significantly pre-flow to post-flow. However, detritus cover percentage was significantly lower post-flow compared to pre-flow where tadpoles were actually observed (GANDA 2004b). No effort was made in 2003 to systematically sample the effects of high recreational flows on detritus at defined sample locations. 2004 Pilot Study In July 2004, a pilot study was conducted to measure the effects of the 1,200 cfs recreational flow on the amount of detritus and algae present at specific sampling locations co-located with tadpole habitats at known FYLF breeding sites in the Cresta Reach. Thirty-five shallow, edgewater quadrats (subplots) were sampled at seven subsites both before and after the July recreational flow. Percent cover of detritus and algae were recorded within 24 to 48 hours before and after the flow event. Often detritus covered a portion of the algae growth, and every effort was made to estimate total cover for both algae and detritus separately. The size of each sampling quadrat was 0.1 square meter (1 square foot). A 0.1 m2 portion of a Plexiglas viewing plate with gridlines drawn to divide the plate into 100 equal-sized squares was used. When sampling, the number of squares (out of 100) with ≥50 percent detritus (or algae) showing on the substrate directly underneath were counted (i.e, if most of the square was covered, it was counted). The total number of squares meeting this criterion were then recorded onto data sheets and equated directly to percent cover. A dusting of detritus did not qualify since this would not provide any cover for tadpoles. Although some rocks appeared green with algae stain, only the presence of algae cells smooth to the touch was recorded. Fixed-location quadrats were marked (on the lower-right corner) with painted rocks embedded into the substrate to ensure that pre- and post-flow sampling locations were the same.

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A stratified sampling system was used to select locations along the bars that were likely to receive either low (0-20 cm/sec) or high (>20 cm/sec) flow velocities during the recreational flow. Approximate locations of these general flow classification areas were known from previous observations of staff gages installed for recreational flows in 2002 and 2003. Sample locations were also visited during the recreational flow to visually estimate surface flow velocities and confirm the criteria used for stratification. At each cobble bar subsite (N = 7), the quadrats were established in general areas where tadpoles had been previously observed, and quadrats included areas in either of the two surface flow velocities mentioned above. Velocity at base flow at all subplots were less than 5 cm/sec. Quadrats were mapped by distance (determined with a rangefinder) from the bottom (or downstream portion) of each subsite and were placed in edgewater tadpole habitats typically utilized by FYLF tadpoles in the Cresta Reach (i.e., closer than 50 cm from the wetted edge at base-flow with depths ranging from 10-30 cm). In addition, quadrats were placed in areas where at least some algae and detritus were present. We did not enter the river near quadrats during recreational flows to avoid disturbing sediments. The same observer made all cover estimates before and after the recreational flow for consistency. Prior to each sampling effort, the quadrat was scanned through the viewer and prodded gently with a finger to help determine the presence of algae under detritus, detritus and algal thickness, and to help differentiate between algal growth and detritus. Data Analysis The following hypotheses were tested by paired t-test:

Ho: Before Average % Cover = After Average % Cover Ha: Before Average % Cover does not = After Average % Cover

The significance level of 0.05 was used for paired t-tests. Tests assessed whether: (1) there were statistically significant changes in the percent cover of algae and detritus (separately) from pre-flow to post-flow in the pooled data (includes both low and high exposure-to-flow locations); and (2) there were statistically significant changes in the percent cover of algae and detritus (separately) from pre-flow to post-flow for the low and high exposure-to-flow locations separately. In other words, one test compared the overall data combining both low and high flow exposure sites, while the other test compared the stratified samples to determine if there was a difference between exposure locations. Data sheets for the detritus study are provided in Appendix 10.

2.8 FYLF Fungal Egg Mass Testing During field observations on the Cresta Reach in 2002-2003 egg masses were found that appeared infected by fungus (ovum were white rather than black in color). In 2004, we collected and preserved three small portions of egg masses that exhibited similar signs in

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order to identify the suspected fungus. Two masses were sampled (~ 20 eggs each) from the Cresta Reach: 1) egg mass “A” from Subsite 9d collected on 29 May 2004, and 2) egg mass “A” from Subsite 9a collected on 5 June 2004. Another egg mass was sampled from the Poe Reach: egg mass “A” from Subsite 6c collected on 8 May 2004. Samples collected by Kevin Wiseman and Ron Jackman were subdivided into two portions and preserved in either 95% ethanol or formalin. On 28 September 2004, samples were delivered for analysis to Dr. John Parker, D.V.M. at U.C. Berkeley. Samples were analyzed using a compound microscope.

2.9 Garter Snake Predation Study While conducting VES in the Project area in 2003-2004, we used methods described by Fitch (1987) to palp garter snakes (primarily the Sierra garter snake, Thamnophis couchii) in order to document predation on FYLF. Snakes were captured by hand and inspected for prey items in the stomach by gently squeezing the snakes body, moving from the lower two-thirds of the body towards the head to force regurgitation of prey items (palping). When possible, snakes with prey items were measured (total length or snout-vent length) and weighed using a Pesola scale, and stomach contents were preserved in 70 percent ethanol for later identification and verification. Snakes that were palped and yielded no stomach contents were also recorded. Data were recorded in field notebooks or on VES data sheets (Appendix 6).

2.10 2003 Tadpole Attrition Study During late May and early June 2002, we observed a substantial decrease in numbers of tadpoles around two egg mass sites on the Cresta Reach. This decrease occurred over a seven-day period that coincided with the June 2002 recreational flow (GANDA 2004a). Because no data were available on natural dynamics of FYLF tadpoles, we proposed a study for 2003 to measure the natural rate of observable decline in the absence of a manufactured flow release (i.e., whitewater recreational flow). The goal of the tadpole attrition study was to estimate the average rate of observable decline in tadpole numbers per day. During the 2003 survey season, we performed multiple counts of 16 tadpole groups, including 11 groups on the Cresta Reach and five groups on the Poe Reach in conjunction with studies for the Poe Hydroelectric Project (GANDA 2004c). Each tadpole group was counted once per day for between three and seven days within a 10-day period. Count data were tabulated and graphed to show the changes in tadpole numbers over time. Where double counts were recorded for a tadpole group on a particular day, we used the mean value of the two counts for data analysis. An overall attrition rate was determined using two methods. First, a linear regression model was applied to the combined tadpole counts for all 16 groups. Second, we computed a weighted average slope from the

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regression line slopes for each individual tadpole group. Finally, we calculated the average attrition rate for the Cresta and Poe reaches separately. Prior to data analysis, we discarded increasing counts that were collected at some groups. In these cases, we realized that egg masses were still hatching larvae daily, thereby increasing the numbers for a period of several days. For the 16 groups that were analyzed, Day One represented the highest count before the numbers began to decline. Because the amount of cover varied between tadpole group count sites, notes were taken on the relative amount of cover present and available to tadpoles. Aquatic cover consisted mostly of layers of detritus in which the tadpoles could at least partially bury themselves, and crevices between boulders. During the counts, no attempt was made to stir up detritus or probe into crevices, since the object of the study was to determine the rate of observable decline or attrition in tadpole numbers. Tadpole attrition data sheets are provided in Appendix 9 of the 2003 monitoring report (GANDA 2004b). An observer bias study using duplicate blind counts by two observers was conducted simultaneous with the tadpole attrition study in 2003. The results of this study determined that there was no statistical difference between counts of recently-hatched tadpoles by different observers (see GANDA 2004b). 3.0 RESULTS 3.1 Habitat Assessments This section describes pertinent habitat features at 18 subsites based on the information gathered during habitat assessments, including 12 conducted on the Cresta Reach and six conducted on the Rock Creek Reach (Table 3.1-1). Completed Habitat Assessment Data Sheets for each site are provided in Appendix 3. Preliminary habitat assessments were conducted in 2001 at several subsites within the Project area (ECORP 2002; Table 3.1-1). Table 3.1-1. Subsites within the Rock Creek-Cresta Project Area for which habitat assessments were conducted from 2001-2004. Cresta Reach Rock Creek Reach 2001 (ECORP 2002) 1a, 1b, 1c, 2 3, 4a, 4b, 4c, 5 2002 1a, 1b, 1c, 1d, 6b, 9a, 9e 3b, 3c, 5b, 5c 2003 6a, 6c, 9d 4a, 8 2004 9b --- General upland habitat for the Cresta and Rock Creek reaches is characterized as foothill hardwood/conifer, consisting of ponderosa pine (Pinus ponderosa), oaks (Quercus spp.),

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and incense cedar (Calocedrus decurrens). Common shrub species include bitterbrush (Purshia tridentata), whitethorn (Ceanothus cordulatus), western serviceberry (Amelanchier utahensis), and manzanita (Arctostaphylos sp.). General riparian species include white alder (Alnus rhombifolia), willow (Salix sp.) and sedge (Carex sp.). The elevation ranges from 439 m (1,440 ft.) at the Cresta Powerhouse Area (Site 6) on the lower Cresta Reach to 658 m (2,160 ft.) at Site 8 on the upper Rock Creek Reach. Other aquatic species commonly observed include hardhead (Mylopharodon conocephalus), Sacramento pike minnow (Ptychocheilus grandis), Sacramento sucker (Catostomus occidentalis), rainbow trout (Oncorhynchus mykiss), smallmouth bass (Micropterus dolomieui), Sierra garter snake, and signal crayfish. Bullfrogs have not been observed in the Cresta or Rock Creek reaches of the NFFR.

3.1.1 Habitat Assessments- Cresta Reach 3.1.1.1 Site 1 – Shady Rest Area Site 1 is located adjacent to the Shady Rest Area off Highway 70 on the NFFR. Site 1 consists of four subsites: 1a, 1b, 1c, and 1d. The four subsites total 504 m along a 900 m reach, including two lateral cobble bars, a point bar, and a boulder/cobble island at a pool tail-out. All four subsites are at approximately 457 m (1,500 ft.) elevation. Subsite 1d is at the upstream end of Site 1, with Subsites 1a, 1b, and 1c following in respective order moving downstream (Figure 1.0-1; Appendix 4). Subsites 1a and 1d had the least amount of vegetation at the margin (10%), while Subsite 1c had substantial amounts of vegetation (60%). All subsites within Site 1 lacked a dense riparian canopy and received abundant direct sunlight. Subsite 1c was considered to be relatively poor-quality breeding habitat for FYLF, because higher base flows inundated much of the pool tail-out island area. The potential for FYLF breeding at Subsite 1b was considered poor to moderate, mostly due to narrow edgewater, deep waters in the adjacent submerged bar areas increasing access for predatory fish, and relatively dense vegetation at the margin. We considered Subsites 1a and 1d to contain the most favorable habitat for FYLF with minimal amounts of shoreline vegetation, and ideal cobble/boulder substrate and edgewater microhabitat characteristics. Subsite 1a The habitat assessment for Subsite 1a was conducted on 8 October 2002. ECORP (2002) also conducted a habitat assessment in 2001. This subsite consists of a 231 m long, mostly low-to-moderate bank gradient, lateral cobble bar situated on the right bank adjacent to low-gradient riffle (60%), run (30%), and pool tail-out (10%) river habitat. Aquatic substrate (moderately embedded) consisted of boulders (50%), with cobble (30%), gravel and sand (each 10%). Water velocities ranged from 0 to 20 cm/s in this area, generally increasing towards the downstream end of the subsite where low-gradient riffle predominated. The downstream end of Subsite 1a contained a few small, backwater

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pools that collected water following pulse flows, and were utilized by juvenile FYLF. Sparse margin vegetation was dominated by forbs and included grasses, sedge (Carex sp.), and willows (Salix sp.); emergent and overhanging vegetation consisted of willows. The edgewater habitat covered an area approximately 500 m2 with an average depth of 20 cm, which led to an inundated river bar that covered approximately 1,000 m2 and averaged 1 m deep. The bank changed from low (20 cm/sec in this area, with higher velocities concentrated at the edge of the island near the channel. Higher base flows in 2002 (approximately 250 cfs) flooded some of this subsite compared to 2001 and previous years, resulting in reduced amounts of exposed substrate (Alicia Pool, pers. comm. 2002). Margin vegetation along the right bank (60% covered) was dominated by willow, and included grass, sedge and forbs. Emergent vegetation on the island (20%) and overhanging vegetation (20%) consisted primarily of willows, with some sedge. Edgewater habitat covered an area approximately 335 m2 with an average depth of 15 cm.

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Inundated river bar covered approximately 220 m2 and averaged 30 cm deep. Potential amphibian cover at Subsite 1c consisted mainly of gaps between substrate (both aquatic and terrestrial), leaf litter, woody debris, vegetation, and algae. The closest tributary to this subsite (Bear Creek) is located on the opposite bank, about 225 m downstream. Subsite 1d The initial habitat assessment was completed on 28 May 2002. Subsite 1d, located just downstream of Arch Rock Tunnel, consists of a 141 m low-gradient point bar situated on the left bank along side run (80%), low-gradient riffle and pool tail-out (both 10%) river habitats. Aquatic substrate (moderately embedded) consisted mainly of boulders (50%) with cobble (30%), gravel, and sand (each 10%). Water velocities ranged from 0 to 10 cm/s in edgewater and submerged bar portions of this site. The very sparse vegetation at the shore margins consisted primarily of sedge; sparse emergent vegetation consisted mainly of grass and sedge. Edgewater habitat was 2-5 m wide and covered an area approximately 490 m2. Average depth was 15 cm. The inundated portion of the river bar covered approximately 980 m2 and averaged 40 cm in depth. The bank at Subsite 1d was low-gradient. Potential amphibian cover consisted of gaps between substrate (both aquatic and terrestrial) and woody debris. The closest tributary to this subsite is located about 190 m downstream from the bottom of the site, though a small, intermittent tributary comes in at the middle of the site. Site 2 – NFFR Downstream of the Confluence with Grizzly Creek The initial habitat assessment was completed on 24 July 2001 by ECORP (2002) biologists. Site 2 is located 30 m downstream of the confluence with Grizzly Creek in the Cresta Reach of the NFFR. The site is situated adjacent to Highway 70 and is 225 m in length. Potential FYLF habitat was found primarily along the right bank, which was characterized as a partially-inundated, low-gradient boulder/cobble bar. The right bank area was predominantly shallow riffle habitat with low water velocity (

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elevation, the lowest elevation in the Project area. We considered this site to contain moderate quality habitat for breeding FYLF due to its minimal (10%) amount of marginal vegetation and favorable substrate composition. High velocities in edgewaters along the downstream portion of the site reduced the potential for FYLF oviposition; however, the upstream portion of the site had favorable edgewater microhabitats with low water velocities suitable for FYLF breeding. Subsite 6a The initial habitat assessment was completed on 12 June 2003. Subsite 6a consists of a 354 m, low bank gradient cobble boulder island situated on the left bank of the island along a side channel with run/glide (50%), pool (40%), and riffle (10%) river habitat. Aquatic substrate (slightly embedded) consists mainly of cobble (50%), boulder (30%), some gravel/pebble (10%) and sand (10%). Three riffle sections of this side channel separate pools and create a river gradient change. The largest riffle area near the downstream end of the site stretches approximately 20 m. Water velocities ranged from 0 to 24 cm/sec with the highest velocities at and near the riffles. During the habitat assessment, shoreline vegetation was moderate to high along most of the subsite and dominated by willow, alder, grass and blackberry. Emergent vegetation was sparse overall and consisted mostly of sedge. Edgewater habitat covers an area approximately 450 m2 with an average depth of 1-1.5 m. The inundated river bar covers approximately 20 m2 at the top of the site and averages less than one meter in depth. Bank gradient is low (20 cm/s along the cobble bar, with the highest velocities concentrated near the downstream end of the subsite. Shoreline vegetation was sparse in most places and dominated by forbs with grass, sedge and willows. Emergent vegetation was sparse overall and consisted of sedge. Edgewater habitat covered an area approximately 90 m2 with an average depth of 15 cm. The inundated river bar covered approximately 180 m2 and averaged 25 cm deep. Bank

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gradient was low. Moderate density potential amphibian cover at Subsite 6b consisted of gaps between substrate (both aquatic and terrestrial), woody debris, and algae. The closest tributary to this subsite is located at the bottom of the site. Subsite 6c The initial habitat assessment was completed on 12 June 2003. Subsite 6c consists of a 179 m long, high gradient cobble/boulder bar situated on the right bank of the island along the main river channel with run/glide (90%) and riffle (10%) river habitat. Aquatic substrate (

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area. Margin vegetation was composed primarily of forbs and sedge, although growth was sparse (10% cover). Equally sparse emergent vegetation consisted primarily of sedge with interspersed forbs. The edgewater habitat covered approximately 60 m2 with an average depth of 25 cm, and the inundated river bar covered approximately 75 m2, with depths averaging 30 cm. The right bank was low gradient. Potential aquatic and terrestrial amphibian cover at Subsite 9a (both 30%) consisted of gaps between substrate and some vegetation. The closest tributary to this subsite is a small, overgrown drainage that comes in at the bottom; however, a larger stream is located about 95 upstream from the top of the subsite. Subsite 9b The initial habitat assessment was completed on 22 October 2004. Subsite 9b is a 105 m low-gradient lateral cobble bar located on the right bank of the NFFR. The subsite is found within run (50%), pool (30%), and riffle (20%) river habitat. Aquatic substrate (moderately embedded) consists mainly of cobble (40%), boulder, gravel and sand (each 20%). Water velocities were estimated to range from 0 to 20 cm/sec. Margin vegetation is found at this subsite in high densities (80%), consisting primarily of sedges, as well as willow and alder. Edgewater habitat covered approximately 240 m2 with an average depth of 20 cm. The inundated river bar covered an area approximately 120 m2 with an average depth of 20 cm. Bank gradient was low (< 15°) on the right bank. There are high amounts of amphibian cover consisting of aquatic vegetation and gaps between substrate. Terrestrial cover is found in moderate amounts, consisting primarily of gaps between cobbles, boulders and vegetation. The closest tributary to this subsite is located on the opposite bank, about midway along the site. Subsite 9d The initial habitat assessment was completed on 24 June 2003. Subsite 9d is a 130 m long, moderate-gradient point bar located on the right bank of the NFFR. The subsite is found within run (70%), riffle (20%) and pool (10%) river habitat. Aquatic substrate (slightly embedded) consists mainly of boulder (60%), some cobble (20%), some gravel/pebble (10%) and sand (10%). Water velocities ranged from 0 to 4 cm/sec. During the habitat assessment, shoreline vegetation was sparse along most of the subsite and consisted of forbs, grass, and some willow. Emergent vegetation was very sparse with some grass and sedge. Edgewater habitat covered an area approximately 191 m2 with an average depth of 30 cm. The inundated river bar covered approximately 530 m2 and averaged about 50 cm in depth. Bank gradient was moderate (15-40°) on the right bank. There is high potential aquatic amphibian cover consisting of gaps between substrate and aquatic vegetation (mostly algal). Terrestrial cover is moderate, consisting of cobbles, boulders, and some vegetation. Impacts to amphibian habitat are low at this site. The closest tributary to this subsite is Bear Creek located on the bank opposite the bottom of the site.

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Subsite 9e The initial habitat assessment was completed on 29 May 2002. Subsite 9e is a 77 m long, low-gradient lateral cobble bar located on the left bank of the NFFR, and is adjacent to a long run just upstream of Subsite 9a. Aquatic substrate (moderately embedded) consisted of cobble (40%), boulder (30%), gravel (20%), and sand (10%). Water velocities ranged from 0 to 20 cm/s along the cobble bar. Vegetation growth along the shore margin was moderate and consisted of forbs and sedge interspersed with alder and willow that predominated as overhanging vegetation. Emergent vegetation consisted primarily of sedge and willow, but was relatively sparse. The edgewater habitat covered an area approximately 300 m2 with an average depth of 20 cm. The inundated portion of the river bar covered approximately 200 m2 and averaged 25 cm in depth. The left bank was low gradient. Moderate quantities of potential amphibian cover at Subsite 9e consisted of gaps between substrate (both aquatic and terrestrial) and vegetation. The closest tributary to this subsite is located on the opposite bank, directly across from the bottom of the site.

3.1.2 Habitat Assessments- Rock Creek Reach 3.1.2.1 Site 3 – Indian Jim School Area Site 3 consists of two lateral cobble bars totaling 482 m in length situated on opposite banks of the NFFR near Indian Jim School and upstream of the Tobin Bridge (Figure 1.0-2). Site 3 lies at approximately 609 m (2,000 ft.) elevation and subsite 3c is situated upstream of subsite 3b. No habitat assessments have been completed for subsites 3a and 3d. ECORP (2002) conducted a preliminary habitat assessment for Site 3 in 2001. Subsite 3b had the highest (80%) amount of vegetation along the margin of all monitoring sites within the entire Project area. Subsite 3c also had a relatively high percentage of vegetation (50%). We considered site 3, especially subsite 3b, to have only moderate potential for FYLF occurrence and breeding mainly due the relatively high amounts of shoreline vegetation present, although other features of these cobble bars appeared relatively suitable for FYLF. The wide, shallow edgewater along subsite 3b made it the best overall potential habitat for FYLF in the Rock Creek reach. Subsite 3b The habitat assessment at Subsite 3b was completed on 4 June 2002. Subsite 3b is a 283 m long low gradient lateral cobble bar situated on the left bank of the NFFR along main channel pool (40%), run (also 40%), and low-gradient riffle (20%) river habitat. Aquatic substrate (moderately embedded) consisted of cobble and boulder (both 40%), gravel and sand (each 10%). Water velocities ranged from 0 to 20 cm/s in the near-shore area. The dense, abundant vegetation along the margins was predominately sedge, interspersed with forbs, grass, willow, and alder; emergent vegetation was sparse and consisted primarily of sedge with interspersed willow. The 5 m wide edgewater habitat covered an area approximately 425 m2 with an average depth of 10 cm, and the inundated portion of the river bar covered approximately 800 m2 with an average depth of 20 cm. Potential

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aquatic amphibian cover at Subsite 3b consisted of gaps between substrates and aquatic vegetation (40% overall availability), while terrestrial cover was high (80%) due to the abundant vegetation. The closest tributary to this subsite is located about 75m from the bottom of the site on the left bank. Subsite 3c The habitat assessment at Subsite 3c was completed on 4 June 2002. Subsite 3c consists of a 199 m low-gradient lateral cobble bar situated on the right bank of the NFFR adjacent to run (80%), and pool (20%) river habitat. Aquatic substrate (moderately embedded) consisted of cobble and boulder (both 40%), and gravel (20%). Water velocities ranged from 0 to 15 cm/sec in this area. Vegetation along the margin was moderately dense (40-60% cover) and was dominated by willows interspersed with forbs and sedge; emergent and overhanging vegetation consisted primarily of willow and both covered 30 percent of shallow water habitats. The edgewater habitat ranged from 2 to 10 m wide and covered an area approximately 1,000 m2, with an average depth of 10 cm. The inundated river bar covered approximately 1,000 m2, and averaged 20 cm deep. The right bank was low gradient. Potential amphibian cover at subsite 3c was moderate in quantity for both aquatic and terrestrial habitats (50 and 60%, respectively) and consisted mostly of gaps between substrate and vegetation. The closest tributary to this subsite is Granite Creek about 300 m upstream from the top of the site. 3.1.2.2 Site 4 – Indian Jim Campground Site 4 consists of four subsites (a-d) that total approximately 340 m in length, and is approximately 610 m (2,000 ft.) in elevation. Although Subsite 4a contains features conducive to FYLF breeding, we consider it to have only moderate potential for FYLF. Habitat assessments were not conducted at Subsites 4b, 4c, and 4d.

Subsite 4a The habitat assessment at Subsite 4a was completed on 27 June 2003. Subsite 4a consists of a 103 m, moderate gradient lateral bar situated on the left bank of run (90%) and some riffle (10%) river habitat. Aquatic substrate (moderately embedded) consists of boulder (40%), cobble (30%), with some gravel/pebble, sand and silt/clay (all ~10%). Water velocities ranged from 0 to 5 cm/sec along near-shore areas. Margin vegetation was moderate to high (60-80%) and mostly consisted of forbs, grass, sedge, willow and alder. The emergent vegetation was mostly sedge and some grasses. Edgewater habitat ranged in width between 1-2 m and covered an area approximately 135 m2 with an average depth of 20 cm. Inundated river bar was present and covered approximately 1,200 m2, with an average depth of 50 cm and velocities of 10-35 cm/sec. Potential amphibian cover at Subsite 4a was high (80%) and consisted mostly of gaps between substrate and aquatic vegetation. Terrestrial cover was moderate (50%) with woody debris and vegetation comprising the dominant features. The closest tributary to this subsite is Granite Creek located on the bank opposite the top of the site.

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3.1.2.3 Site 5 – Rodgers Flat Area Site 5 consists of three subsites totaling 244 m, including a point bar and a lateral cobble bar, situated on opposite banks of the NFFR upstream of Rodgers Flat. Subsite 5b is approximately 658 m (2,160 ft.) in elevation, with subsite 5c at 664 m (2,180 ft.) elevation. Subsite 5a was not included in this study. ECORP (2002) conducted preliminary habitat assessment for Site 5 in 2001. Subsites 5b and 5c had relatively high amounts of margin vegetation (60% and 50%, respectively), and were the only sites in the study that contained silt/clay (10%) in the substrate. Although both subsites contained features conducive to FYLF breeding, we considered them to have only moderate potential for FYLF. Subsite 5b The habitat assessment at Subsite 5b was completed on 29 May 2002. Subsite 5b consists of a 144 m long, low-gradient lateral cobble bar situated on the right bank adjacent to pool (90%) and low-gradient riffle (10%) river habitat. Aquatic substrate (moderately embedded) consisted of cobble (40%), boulder (30%), and gravel, sand and silt (each 10%). Water velocities ranged from 0 to 5 cm/sec along near-shore areas. Margin vegetation was moderate in density (50%) and was dominated by forbs interspersed with grass, sedge, and willows. The sparse emergent vegetation consists primarily of grasses with sedge and willows. The shallow edgewater habitat ranged in width between 1-10 m and covered an area approximately 550 m2 with an average depth of 20 cm. The inundated portion of the bar was expansive at this site and covered approximately 715 m2 with an average depth of 60 cm. The right bank was moderate gradient. Potential amphibian cover at subsite 5c consisted of gaps between substrate (both aquatic and terrestrial), woody debris, and aquatic vegetation. The closest tributary to this subsite is located on the opposite bank just downstream of the bottom of the site. Subsite 5c The habitat assessment at Subsite 5c was completed on 29 May 2002. Subsite 5c consists of a 100 m long, low-gradient point bar situated on the left bank of the NFFR near pool tail-out (70%), low-gradient riffle (20%), and run (10%) river habitat. Aquatic substrate (moderately embedded) consisted of cobble (40%), boulder (30%), and gravel, sand and silt (each 10%). Water velocities ranged from 0 to 20 cm/sec in this area. Vegetation along the margin was relatively dense (60%) and dominated by forbs interspersed with grass, sedge, willow, alder and cottonwood; emergent and overhanging vegetation were sparse and consisted primarily of willows. The edgewater habitat (2-5 m wide) covered an area approximately 350 m2 with an average depth of 20 cm, while the inundated portion of the bar covered approximately 800 m2, and averaged 40 cm in depth. The left bank was low gradient. Potential amphibian cover at subsite 5c consisted of gaps between substrate, and vegetation, though neither aquatic nor terrestrial cover potential was very high (20% and 49%, respectively). The closest tributary to this subsite is located on the opposite bank, about 100 m upstream from the top of the site.

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3.1.2.4 Site 8 – Rock Creek Dam Area The habitat assessment at Subsite 8 was completed on 27 June 2003. Site 8 consists of one small area located at the gauging station below Rock Creek Dam. It is a 57 m long, moderate-gradient lateral bar situated on the right bank adjacent to a pool (60%), run (40%) river habitat. This site is approximately 664.5 m (2,180 ft.) in elevation, the furthest upstream of monitoring sites in the entire Project area. Aquatic substrate (moderately embedded) consists mostly of sub-angular boulder (50%), cobble (30%), and sand (20%). Water velocities ranged from 0 to 5 cm/sec along near-shore areas. Margin vegetation was moderate to high in density (60-80%) and was dominated by forbs grass, sedge, alder and willows. The sparse emergent vegetation consisted primarily of grasses with sedge and a few willows. The edgewater habitat ranged in width from 1-2 m, and covered an area approximately 98 m2 with an average depth of 30 cm. The inundated portion of the bar at this site covered approximately 142 m2 with an average depth of 45 cm. The right bank was moderate gradient. Potential aquatic amphibian cover at Site 8 consisted of gaps between substrate and aquatic vegetation. Terrestrial cover is mostly vegetation, with some woody debris and leaf litter. Overhanging vegetation (willow, alder) was moderate. We considered Site 8 to have moderate quality habitat for FYLF. The closest tributary to this subsite is located on the opposite bank, just upstream from the top of the site.

3.2 Visual Encounter Survey Results Results of 2004 Cresta Reach VES are described in two sections: 1) by FYLF life stage (Sec. 3.2.1), and 2) by site (Sec. 3.2.2). In addition, comprehensive Project (2002- 2004) results are included within each section for comparison. No FYLF were observed within the Rock Creek Reach (Section 3.6), and monitoring during recreational flows was not conducted in that reach during 2004. The following results are for the Cresta Reach only.

3.2.1 VES Results by FYLF Life Stage 3.2.1.1 Egg Masses Egg mass distribution In 2004, egg masses were first documented in the Cresta Reach on 19 May 2004. During 2004 surveys, a total of 31 egg masses were observed at eight subsites within the Cresta Reach. Twelve egg masses (39% of total) were observed at Site 1 (Shady Rest Area), seven egg masses (22%) at Site 6, and twelve egg masses (39%) at Site 9 (Fig. 3.2-1). From 2002-2004, a total of 66 egg masses were observed at nine subsites within the project area. Twenty egg masses (30% of total) were observed at Site 1, sixteen egg masses (24%) at Site 6, and thirty egg masses (45%) at Site 9 (Fig. 3.2-1). Subsites 1a, 1d, 6b, 9a and 9e were surveyed all three years. Subsites 6a, 6b, 9b and 9d were

surveyed in 2003 and 2004. Site 2 and subsites 1b, 1c, 6c, and 9c were also searched but no egg masses were found in 2004.

Figure 3.2-1. FYLF egg mass distribution and frequency on the Cresta Reach, North Fork Feather River, 2002-2004.

0

1

2

3

4

5

6

7

8

9

1A 1D 6A 6B 6C 9A 9B 9D 9ESubsite

Num

ber o

f egg

mas

ses

2002 (n=7)2003 (n=28)2004 (n=31)

Egg mass habitat parameters In 2004, egg masses (N = 31) were deposited an average distance of 2.4 m from shore (range = 0.1 to 5.8 m; SD = 1.5 m) and 30 cm deep (range = 12 to 52 cm; SD = 11cm) (Table 3.2-1; Figure 3.2-2). Maximum water depths at egg mass locations averaged 36 cm (range 14 – 58 cm; SD = 12). Mean water velocity measured at egg masses was 4.2 cm/sec (range = 0-15 cm/sec; SD = 5.2) during initial observations. Mean surface water velocity recorded above egg masses was 11.3 cm/sec (range = 0-40 cm/sec; SD = 12.9). Water temperatures at egg masses averaged 16.7 °C (range = 14.4 –18.4 °C; SD = 1.1).

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27



Table 3.2-1. Summary of FYLF oviposition site habitat parameters in the Cresta Reach, 2004 and 2002-2004. Distance

from shore (m)

Egg mass depth (cm)

Max. Depth at egg mass

(cm)

Velocity at egg mass

(cm/sec)

Surface1 velocity

above egg mass

(cm/sec)

Water Temperature

(° C)

2004 (N = 31) Mean 2.4 30 36 4.2 11.3 16.7 Standard Dev. 1.5 11 12 5.2 12.9 1.1 Range 0.1 – 5.8 12- 52 14-58 0- 15 0- 40 14.4- 18.4 2002-2004 (N = 64) Mean 2.4 30 37 3.6 8.8 16.8 Standard Dev. 1.9 11 12 4.9 11.0 1.2 Range 0-10.0 10-57 14-64 0-18 0-40 14.4- 19.0 1Surface velocity was recorded in 2003 and 2004 only Since two of the egg masses from the 66 total that were detached and the attachment point could not be located, only 64 egg masses were included in this depth and distance-from-shore analysis. From 2002-2004, egg masses (N = 64) were deposited an average distance of 2.4 m from shore (range = 0 to 10.0 m; SD = 1.9 m) and 30 cm deep (range = 10 to 57 cm; SD = 11 cm) (Table 3.2-1; Figure 3.2-3). Maximum water depths at egg mass locations averaged 37 cm (range = 14 – 64 cm; SD = 12). Mean water velocity measured at egg masses was 4 cm/sec (range = 0-18 cm/sec; SD = 5) during initial observations. Mean surface water velocity recorded at egg mass sites was 8.8 cm/sec (range = 0-40 cm/sec; SD = 11.0). Water temperatures at egg masses averaged 16.8 °C (range = 14.4 –19.0 °C; SD = 1.2).

Figure 3.2-2. Distance from shore and corresponding depths of egg mass and stream bottom for 31 FYLF egg masses observed in the Cresta Reach, NFFR, 2004.

0

10

20

30

40

50

60

70

0 1 2 3 4 5 6 7

Distance from Shore (m)

Dep

th (c

m)

Egg MassStream Bottom

28



egg masses shared measurements, these multiples are shown with larger symbols.

Figure 3.2-3. Distance from shore and corresponding depths of egg mass and stream bottom for 66 FYLF egg masses observed in the Cresta Reach, 2002-2004. If two

0

10

20

30

40

50

60

70

0 2 4 6 8 10 12

Distance from Shore (m)

Dep

th (c

m) Stream Bottom

Egg Masses

Multiple (2) EggMassMultiple (2)Stream Bottom

29



nd

2002-2004, a total of 66 egg masses were observed, although each parameter was

In 2004, egg masses (N = 31) were attached primarily to boulder (45% of total) abedrock (35%) substrates; other substrates used for attachment were cobble (13%), and woody debris (7%). Percentage of silt buildup on egg masses was mostly less than 25 percent (59% of total egg masses) or none (21%). Four egg masses had 25-50 percent silt (14%) and two had greater than 50% silt (6%). Egg masses were most commonly placed underneath attachment substrates (26%) with a streamside orientation (also 26% of masses). Forty-eight percent of egg masses were positioned so that they received flow alongside the egg mass (shear flow). Six egg masses (19% of total) were deposited in areas with no water velocity. Eighty-one percent of egg masses were located in edgewater microhabitats. Boulder/cobble substrates were most common adjacent to 14 of 31 egg masses (45%). Fifty-two percent of egg masses in 2004 were located in run mainstream habitats, and 35 percent were located next to main channel pools (Table 3.2-2).

romFnot always measured on the total (Table 3.2-2). Thirty-four (55%) of these egg masses were attached to boulders, eleven (16%) were attached to cobbles, twelve (19%) were attached to bedrock, and five (10%) were attached to either woody debris or found initially detached. Most egg masses (57%) were initially observed with

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Table 3.2-2. Summary of habitat characteristics associated with FYLF egg masses in the Cresta Reach, NFFR in 2004 and from 2002-2004. Predominant characteristic types are highlighted in bold. Total number of samples measured in parentheses.

2004 Egg Masses (N = 31)

2002-2004 Egg Masses (N = 66)

Habitat Characteristic Number of egg masses

Percent of total

Number of egg masses

Percent of total

Boulder 14 (N = 31) 45 34 (N = 62)1 55 Cobble 5 13 11 16 Bedrock 11 35 12 19

Attachment substrate

Other 1 7 5 10 0 6 (N = 29) 21 13 (N = 60) 22

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Observations of egg masses using snorkeling In 2003 and 2004, snorkeling was used as an additional VES method to increase our ability to find egg masses, particularly in deeper and swifter microhabitats; snorkeling was not used in the 2002 surveys. Of the 59 egg masses recorded in 2003-2004, 20 (34% of 2003-2004 egg masses) were found while snorkeling. While snorkeling, egg masses were discovered an average of 3.5 m from shore, compared to 1.9 m from shore while wading. Additionally, egg masses were found at 39 cm depth (26 cm when wading), 46 cm maximum depth at egg mass sites (33 cm when wading), 5.0 cm/sec water velocity (2.8 cm/sec when wading), and 9.3 cm/sec surface velocity (8.5 cm/sec when wading). There was only a slight difference in water temperatures at egg masses discovered by snorkeling or wading (Table 3.2-3). In 2003, 11 of 28 egg masses (39% of total) were found using the snorkeling method. Of these, approximately one-half would likely have been found with conventional wading search techniques. However, five egg masses at Subsite 1a were found in habitats previously considered by our survey crew to be unsuitable and in areas that would have been extremely difficult to survey by conventional wading techniques. These habitats were characterized as low-to-moderate gradient riffle/pocket water up to 10 m from shore. Flow velocities exceeded 50 cm/sec. in the swift-flowing channels between boulder pockets. In 2004, nine of 31 egg masses (29% of total) were found using the snorkeling method. It is likely that some of the nine egg masses may have been discovered using conventional wading techniques. However, some of these egg masses may not have been discovered if the snorkeling method was not utilized, including two masses at Subsite 6a (in swift currents) and several of the masses at Subsite 9a, where a high-gradient edgewater made egg mass searches via wading difficult. Table 3.2-3. Summary of 2003-2004 egg masses discovered using snorkeling versus conventional wading techniques. 2003-2004 egg masses (N = 59)

Distance From

Shore (m)

Egg Mass Depth (cm)

Max Depth (cm)

Velocity at Egg Mass

(cm/sec)

Surface Velocity (cm/sec)

Water Temp. (°C)

Average 3.5 39 46 5.0 9.3 16.9 Snorkeling (N = 20) SD 2.6 8 10 4.5 9.2 0.8

Average 1.9 26 33 2.8 8.5 17.0 Wading (N = 39) SD 1.2 11 12 4.6 1

DATA REPORT€¦ · Appendix 2: A Standardized Approach for Habitat Assessments and Visual Encounter Surveys for the Foothill Yellow-Legged Frog (Rana boylii) (Seltenrich and Pool

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