Western Riverside County Multiple Species Habitat Conservation Plan (MSHCP) Biological Monitoring Program

Stream Survey Report 2007

18 MARCH 2008 Stream Survey Report 2007

TABLE OF CONTENTS INTRODUCTION...... 1

Survey Goals...... 1

Arroyo Toad (Bufo californicus; “BUCA”)...... 1

Coast Range Newt (Taricha torosa torosa; “TATO”) ...... 2

California Red-legged Frog (Rana aurora draytonii; “RAAU”) ...... 2

Mountain Yellow-legged Frog (Rana muscosa; “RAMU”)...... 2 METHODS ...... 3

Protocol Development ...... 3

Personnel and Training ...... 3

Study Site Selection...... 4

Survey Methods ...... 4 RESULTS ...... 5

Arroyo Toad (BUCA)...... 7

Coast Range Newt (TATO) ...... 10

California Red-legged Frog (RAAU) ...... 13

Mountain Yellow-legged Frog (RAMU)...... 13

Habitat Conditions ...... 14 DISCUSSION ...... 14

Recommendations for Future Surveys...... 15 REFERENCES...... 18

LIST OF TABLES AND FIGURES

Table 1. Core Area designation by species (denoted with ‘X’) and whether or not each area was surveyed in 2007...... 5

Table 2. Survey locations, dates, and amphibian species during stream surveys in 2007...... 6

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Table 3. Habitat characteristics for stream survey locations in 2007...... 8

Table 4. Coast range newt (TATO) detections in 2007. Note that abundances are estimates. .... 10

Table 5. Habitat characteristics at TATO locations...... 12

Figure 1. Start locations for stream reaches surveyed in 2007...... 16

Figure 2. Coast range newt (TATO) detections along stream survey reaches in 2007...... 17

LIST OF APPENDICES

Appendix A: USGS Stream Survey Protocol...... 19

Appendix B: Monitoring program hardcopy datasheets...... 43

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NOTE TO READER: This report is an account of survey activities undertaken by the Biological Monitoring Program for the Western Riverside County Multiple Species Habitat Conservation Plan (MSHCP). The MSHCP was permitted in June 2004. The Biological Monitoring Program monitors the distribution and status of the 146 Covered Species within the Conservation Area to provide information to Permittees, land managers, the public, and the Wildlife Agencies (i.e., the California Department of Fish and Game and the U.S. Fish and Wildlife Service). Monitoring Program activities are guided by the MSHCP species objectives for each Covered Species, the information needs identified in MSHCP Section 5.3 or elsewhere in the document, and the information needs of the Permittees. While we have made every effort to accurately represent our data and results, it should be recognized that our database is still under development. Any reader wishing to make further use of the information or data provided in this report should contact the Monitoring Program to ensure that they have access to the best available or most current data. The primary preparer of this report was the 2007 Herpetology Program Lead, Natalie Marioni. If there are any questions about the information provided in this report, please contact the Monitoring Program Administrator. If you have questions about the MSHCP, please contact the Executive Director of the Western Riverside County Regional Conservation Authority (RCA). For further information on the MSHCP and the RCA, go to www.wrc-rca.org.

Contact Info: Executive Director Western Riverside County Regional Conservation Authority 4080 Lemon Street, 12th Floor P.O. Box 1667 Riverside, CA 92502-1667 Ph: (951) 955-9700 Western Riverside County MSHCP Monitoring Program Administrator c/o Karin Cleary-Rose 4500 Glenwood Drive, Bldg. C Riverside, CA 92501 Ph: (951) 782-4238

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INTRODUCTION Four MSHCP Covered amphibian species inhabit stream environments in southern California: arroyo toad (Bufo californicus; “BUCA”), coast range newt (Taricha torosa torosa; “TATO”), California red-legged frog (Rana aurora draytonii; “RAAU”), and mountain yellow- legged frog (Rana mucosa; “RAMU”). Each of these species has specific objectives that require the monitoring of known breeding populations within the Conservation Area once a year for the first 5 years of the permit, or across any consecutive 5 year period (BUCA). The Monitoring Program has been collaborating with the U.S. Geological Survey, Western Ecological Research Center (USGS WERC) and U.S. Forest Service (USFS) on amphibian stream surveys in the Conservation Area since 2003 to reduce overlapping survey efforts and to ensure consistent data collection methods. The purpose of stream surveys is to assess the suitability of stream habitats in the Conservation Area for BUCA, RAAU, TATO, and RAMU and to document breeding locations within species-specific Core Areas and other potentially suitable habitat in the Conservation Area. The species objectives, suitable habitat, and MSHCP-identified Core Areas for each species are described under each species section below. The following were the overall survey goals for 2007: Survey Goals: A) Document breeding locations for BUCA, TATO, RAAU, and RAMU within as many species-specific Core Areas and potential habitat stream segments as possible (Table 1). B) Assess stream habitat (e.g., water quality, upland and riparian vegetation, etc.) across the Conservation Area. C) Refine the stream survey protocol to optimize methods for future surveys. D) Provide data to land managers for use in management decisions. Arroyo Toad (Bufo californicus; “BUCA”) BUCA has narrow habitat requirements, typically being restricted to the middle reaches of third order streams (Dudek & Associates 2003). BUCA are additionally constrained by not inhabiting areas with a landscape slope of greater than 3 percent (Miller and Miller 1936; Sweet 1992). Records of BUCA within the MSHCP Plan Area date from the mid 1930s to early 2000s. BUCA’s specific breeding habitat requirements limit the potential areas they are likely to inhabit. Currently, the known distribution of BUCA in western Riverside County includes: Temecula Creek, Arroyo Seco Creek, Tenaja Creek, Los Alamos Creek, San Jacinto River, Bautista Creek, and Wilson Creek. Many historic records of BUCA locations are taken from incidental sightings during surveys for other amphibian species and do not necessarily reflect habitats most preferred by BUCA (Stebbins 1951; Sweet 1989; Sweet 1992). The species objectives for BUCA require the conservation of 9 Core Areas in the MSHCP Conservation Area. These Core Areas include: 1) San Juan Creek; 2) Los Alamos Creek; 3) San Jacinto River; 4) Indian Creek; 5) Bautista Creek; 6) Wilson Creek; 7) Temecula Creek; 8) Arroyo Seco, and 9) Vail Lake. Species objective 6 for BUCA states:

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…within the MSHCP Conservation Area, Reserve Managers will maintain breeding populations at a minimum of 80 percent of the conserved breeding locations as measured by the presence/absence of juvenile toads, tadpoles, or egg masses across any 5 consecutive years (Dudek and Associates 2003). Coast Range Newt (Taricha torosa torosa; “TATO”) TATO also has narrow habitat requirements and requires specific breeding conditions. Its distribution in the MSHCP Plan Area is limited to the Santa Ana Mountains Bioregion. Terrestrial habitats for this species generally include grassland, woodland, and forest. However, breeding activities are restricted to streams and creeks that exhibit “pool and run” hydrology, with breeding occurring in deep pools and oviposition in slow-moving runs. Core Areas for TATO include the Santa Rosa Plateau and the Santa Ana Mountains Bioregion. Species objective 5 for TATO states: …within the MSHCP Conservation Area, Reserve Managers will maintain occupancy of at least 75% of the occupied coast range newt habitat and determine if successful reproduction is occurring as measured by the presence/absence of larvae or egg masses once a year for the first five years after permit issuance (Dudek and Associates 2003). California Red-legged Frog (Rana aurora draytonii; “RAAU”) Based on recent survey results by the Monitoring Program and by Mark Jennings (Rana Resources), RAAU has no known current distribution within the MSHCP Conservation Area; however, areas of suitable habitat remain. RAAU is typically found in lowland streams, wetlands and pools where dense vegetation surrounds relatively deep water within small (< 300 km2) watersheds. Historically, RAAU occupied Arroyo Seco, San Juan Creek, several sewage treatment pools along the Santa Ana River near Fla-Bob airport (1974 and 1980), a northwest tributary of Arroyo del Torro, an area immediately east of Lake Elsinore, and now-developed upper reaches of Murrieta Creek and Santa Gertrudis Creek. The MSHCP species account for RAAU lists Cole Creek at the Santa Rosa Plateau Ecological Reserve as the only recently occupied known location within the Conservation Area and lists Core Areas as the Santa Rosa Plateau and the Santa Ana Mountains. Species objective 6 for RAAU states: ...within the MSHCP Conservation Area, Reserve Managers will determine if successful reproduction is occurring as measured by the presence/absence of juvenile frogs, tadpoles, or egg masses populations once a year for the first five years after permit issuance and then as determined by the Reserve Management Oversight Committee (Dudek and Associates 2003). Mountain Yellow-legged Frog (Rana muscosa; “RAMU”) RAMU has specific habitat requirements that include perennial streams, creeks and isolated pools found above 370 m in the San Jacinto Mountains. Historically, mountain yellow- legged frogs were also observed in Strawberry Creek, Indian Creek, Black Mountain Creek, and lower sections of the North Fork of the San Jacinto River. Specific Core Areas for RAMU include the North Fork of the San Jacinto River (including Dark Canyon), Hall Canyon and Fuller Mill Creek. Species objective 6 for RAMU states:

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... within the MSHCP Conservation Area, maintain successful reproduction as measured by thepresence /absence of tadpoles, egg masses, or juvenile frogs once a year for the first five years after permit issuance and then as determined by the Reserve Management Oversight Committee as described in Section 6.6 (but not less frequently than every 8 years).

METHODS Protocol Development We used an existing protocol, Aquatic Species and Habitat Assessment Protocol for Southcoast Ecoregion Rivers, Streams, and Creeks, written and distributed by USGS (USGS 2005; Appendix A). The protocol uses a visual encounter and dipnet survey method for detecting all life stages of amphibians, and includes an assessment of habitat characteristics. The protocol requires that we segment all streams in the survey area into 250 m reaches and number them uniquely from downstream to upstream order. The protocol is on file at the Biological Monitoring Program office in Riverside, CA or copies can be obtained by contacting the USGS San Diego Field Station directly. Personnel and Training Some of the members of the 2007 amphibian field crew, including the 2007 Herpetology Program Lead, attended a USGS training session on 29 March 2006 on the use of the USGS stream survey protocol and on identifying anuran (frog and toad) and fish species for our region. Species identification training included slides addressing key distinguishing characteristics between species, in addition to observing live and preserved specimen. We then conducted mock stream surveys in the field, led by USGS biologists, to familiarize surveyors with both field and Personal Digital Assistant (PDA) data collection techniques. In 2007, prior to conducting any formal surveys, all field crew were trained (new crew) or retrained (old crew) by the Herpetology Program lead on the USGS protocol and PDA collection techniques through mock surveys. Biologists conducting stream surveys in 2007 included: • Natalie Marioni, Herpetology Program Lead (Regional Conservation Authority) • Angie Coates (Regional Conservation Authority • Lesley Hanson (Regional Conservation Authority) • Rosina Gallego (Regional Conservation Autority) • Ryann Loomis (Regional Conservation Authority) • Valerie Morgan (Regional Conservation Authority) • Robert Packard (Regional Conservation Authority) • Esperanza Sandoval (Regional Conservation Authority) • Justin Ashby (California Department of Fish and Game) • Isaac Chellman (California Department of Fish and Game) • Ricardo Escobar III (California Department of Fish and Game) • Robert Jones (California Department of Fish and Game) • Nicholas Peterson (California Department of Fish and Game) • Sinlan Poo (California Department of Fish and Game)

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Study Site Selection We conducted surveys within accessible Core Areas for the 4 target amphibian species (BUCA, TATO, RAAU, and RAMU). We chose specific streams based on suitable habitat parameters for BUCA and TATO (not RAAU due to rarity, and not RAMU because USGS surveys were covering the high priority locations) and in areas where evidence of breeding had been observed in previous surveys in 2005 and 2006. We also surveyed additional streams and stream segments to contribute to our ongoing effort to accomplish a complete stream and upland habitat assessment all of the streams in the Conservation Area. Habitat assessments included areas where stream reaches may have been dry at the time of the survey. We did not resurvey any stream reaches that we surveyed during the 2006 season and did not detect any Covered amphibian species. In 2007, we surveyed stream segments in Arroyo Seco Creek, Bautista Creek, Cole Canyon Creek, Cole Creek, Horse Creek, Potrero Creek, San Juan Creek, and San Mateo Canyon and their tributaries. We gave priority for surveys to areas more likely to yield BUCA observations, based on streams where we detected BUCA 2005 and a GIS layer of slope habitat. BUCA habitat is limited by a ≤ 3% stream gradient (Miller and Miller 1936; Sweet 1992). Suitable TATO habitat includes stream sections with slow moving and/or pooling water with surrounding woodland habitat. We then gave higher priority to stream reaches suitable for BUCA and additionally suitable for TATO because of the likelihood that two Covered Species could be detected. We did not target any stream segments for RAAU, though sites where suitable habitat was found were noted to facilitate future nighttime surveys. We visited those segments more likely to yield BUCA observations earlier in the season, during the BUCA breeding season. We conducted habitat assessment surveys more often later in the season when we were not targeting specific species. RAMU surveys were organized by USGS. Monitoring program biologists participated in the USGS survey effort. USGS WERC maintains the data for RAMU surveys. Survey Methods Detailed survey methodology is described in USGS Aquatic Species and Habitat Assessment Protocol for Southcoast Ecoregion Rivers, Streams, and Creeks (USGS 2005) (Appendix 1). All waterways (main creeks and tributaries) to be surveyed were sectioned into 250 m segments, with segment numbers (i.e., Reach 1, Reach 2, etc.) beginning at a downstream confluence with a larger order waterway. At least 2 surveyors conducted visual encounter surveys along stream banks and within the channel from downstream to upstream areas. We conducted all surveys in daylight hours (0800 – 1700 hours). Survey time per segment varied according to streambed characteristics and abundance of amphibians detected. We recorded all data using PDAs except during rare occasions when PDAs malfunctioned and paper datasheets were used (Appendix B). Upon returning to the office, the Herpetology Program Lead uploaded PDA data to an internet server to the USGS Pendragon database housed at the San Diego Field Station. At the beginning and end of each survey segment, we collected data on habitat characteristics. Data collected at the beginning of each surveyed segment included: date, observer, time, general weather description, temperature in shade at 1 m above ground, average wind speed, presence/absence of water, water temperature, pH, dissolved oxygen (concentration and percent), conductivity, wetted depth and width of stream channel, water velocity, number of wetted channel braids and slope. We also took upstream photos at the start of each segment. Data collected at the end of a survey included:

Western Riverside County MSHCP 4 Biological Monitoring Program Stream Survey Report 2007 presence and name of exotic plant species, percent wet length, percent shallow, medium and deep pools, presence and number of plunge pools, presence and type of aquatic refugia, percent of three most common aquatic substrates, and presence and type of recent disturbance. Additionally, within each surveyed segment, we collected data when any amphibian species were detected. At the first encounter of each life stage (i.e., tadpole, juvenile, adult) for all species detected, we recorded UTM coordinates in the PDA, which were automatically linked to landscape and water characteristics for that segment and by date and time. We conducted stream surveys between 29 March and 12 October 2007.

RESULTS We surveyed a total of 161 stream segments from 14 drainages and 32 separate main or tributary branches within 8 species-specific Core Areas and 2 non-core areas (Santa Margarita River and Tenaja Canyon; Tables 1 and 2, Figure 1).

Table 1. Core Area designation by species (denoted with ‘X’) and whether or not each area was surveyed in 2007. When a species was found within one of the surveyed locations, the box is shaded. Location BUCA TATO RAAU RAMU Surveyed in 2007 Core Areas Arroyo Seco Creek X Yes Avenoloca Mesa X No Bautista Creek X No Dark Canyon X Yes Fuller Mill Creek X Yes Hall Canyon X Yes Indian Creek X No Los Alamos Creek X Yes Redonda Mesa X No San Jacinto River X X No San Juan Creek X Yes Santa Ana Mountains X X Yes Bioregion Santa Rosa Plateau X X Yes Temecula Creek X No Vail Lake X No Wilson Creek X No Non-core areas Santa Margarita River Yes Tenaja Canyon Yes

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Table 2. Survey locations, dates, and amphibian species detected during stream surveys in 2007. No. of Other Native Survey Exotic Creek Name Segments BUCA TATO RAAU RAMU Frog/Toad Dates Species Surveyed Spp. Hyla 29 Mar Adobe Creek 6 None Yes None None cadeverina, None – 4 May H. regilla Arroyo Seco 9 – 10 H. cadeverina, 6 None None None None None Creek Apr H. regilla Bluewater 10 May 5 None None None None H. regilla None Canyon 11 – 12 Cole Creek 13 None None None None H. regilla None Apr

18 Apr Cole Creek – 24 10 None None None None None None Trib 3 May Cole Creek 18 May 2 None None None None None None Trib 4 Cole Creek 31 May 4 None None None None None None Trib 5 Cole Creek 19 Apr 7 None None None None H. regilla None Trib 6 22 May Dark Canyon† – 15 4 None None None Yes None None Aug 21 May Dark Canyon – 15 2 None None None Yes None None Trib 1† Aug

10 July Dark Canyon – 15 2 None None None Yes None None Trib 1A† Aug

22 May Fuller Mill – 15 2 None None None Yes None None Creek† Aug

11 July Fuller Mill – 15 1 None None None Yes None None Creek Trib 3† Aug

Hall Canyon† - - None None None None - -

Los Alamos 23-May 4 None None None None None None Canyon Trib 3

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Table 2 continued. No. of Other Native Survey Exotic Creek Name Segments BUCA TATO RAAU RAMU Frog/Toad Dates Species Surveyed Spp.

Los Alamos 17 – 25 5 None None None None None None Canyon Trib 4 May

Los Alamos 2 – 3 H. cadeverina, Rana 6 None None None None Canyon May H. regilla catesbeiana

Los Alamos 27 April Canyon Trib – 29 9 None None None None None None 4A May

San Juan 1-May 2 None Yes None None H. regilla None Creek Trib 2

San Juan 3 – 7 5 None None None None None None Creek Trib 2A May San Juan 30 – 31 7 None None None None None None Creek Trib 3 May R. San Mateo H. cadeverina, catesbeiana, 20-Apr 8 None Yes None None Canyon H. regilla Procambaru s clarkii San Mateo Canyon 2-May 5 None Yes None None H. cadeverina None Trib 11 San Mateo 23-Apr 3 None None None None None None Canyon Trib 2 San Mateo 11-May 6 None Yes None None None None Canyon Trib 7 San Mateo 24 April H. cadeverina, 5 None Yes None None None Canyon Trib 9 – 1 May H. regilla Santa 11 – 12 Margarita 17 None None None None None None October River Tenaja 11 May H. cadeverina, 11 None Yes None None None Canyon – 6 June H. regilla

Wildhorse 26 – 30 4 None Yes None None H. cadeverina None Canyon April † USGS stores and maintains data for these surveys. Missing data represent information unavailable at the time of this report. Arroyo Toad (BUCA) No BUCA of any life stage were detected at any location in 2007 (Table 2). Low personnel availability during species appropriate survey periods only allowed us to survey 3 out

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of 9 Core Areas for BUCA in 2007. Of those 6 areas not surveyed, 2 were also not surveyed in either 2005 or 2006 due to lack of access. Though no BUCA detections were made along any surveyed stream, suitable habitat (average ≤ 3% slope) was found in 11 stream segments (Table 3).

Table 3. Habitat characteristics for stream survey locations in 2007. Most commonly represented upland and riparian community types and average habitat characteristics across all stream survey segments for a given stream. No. of No. Water Shallow Medium Deep Stream Upland Riparian Slope* Velocity Segments of Wet Depth Pools Pools Pools Name Community Communityª (%) (m/sec) Surveyed Segments (m) (%)ª (%) (%) Adobe 1.75 51-75, 26-50, 6 Oak Willow Scrub 6 0.29 0% 0 Creek (4) 76-100% 51-75%

Arroyo Seco Chamise Mule Fat 0, 26-50, 6 2.33 5 0.51 0, 11-25% 0% 0.025 Creek Chaparral Scrub 51-75%

Bluewater Mixed Mule Fat 76- 5 2.2 4 0.15 1-10% 11-25% 0 Canyon Chaparral Scrub 100% Unknown/ Unknown/ Cole Creek 13 Other Other 1.17 4 2.39 1-10% 76-100% 1-10% 0 Grassland Grassland Cole Creek Coast Live 10 Oak 3.28 1 0.34 1-10% 76-100% 0% 0 Trib 3 Oak Unknown/ Unknown/ Other Cole Creek 2 Other Grassland, 3 0 n/a n/a n/a n/a n/a Trib 4 Grassland Coast Live Oak Cole Creek Coast Live 4 Non-native 1 1 - 26-50% 51-75% 26-50% 0 Trib 5 Oak Unknown/ Unknown/ 1-10, Cole Creek 1 1-10, 7 Other Other 2 0.29 11-25% 76- 1.75 Trib 6 (5) 26-50% Grassland Grassland 100% Los Alamos Mixed 3.2 6 Willow Scrub 6 0.26 26-50% 1-10% 0% 0 Canyon Chaparral (5) Los Alamos Mixed 3.5 0, 0, 11- Canyon 4 Willow Scrub 2 1.4 0, 1-10% 0 Chaparral (2) 76-100% 25% Trib 3 Los Alamos Mixed Canyon 5 Oak 2.6 1 n/a n/a n/a n/a n/a Chaparral Trib 4 Los Alamos Mixed Coast Live 6.5 76- Canyon 9 0 0.35 1-10% 0% 0 Chaparral Oak (6) 100% Trib 4A San Juan Coast Live 1 2 Oak 1 0.14 26-50% 26-50% 26-50% 0 Creek Trib 2 Oak (1)

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Table 3 continued. No. of No. Water Shallow Medium Deep Stream Upland Riparian Slope* Velocity Segments of Wet Depth Pools Pools Pools Name Community Communityª (%) (m/sec) Surveyed Segments (m) (%)ª (%) (%) Mixed San Juan Chaparral, Coast Live 3 76- Creek Trib 5 1 0.1 1-10% 1-10% 0 Scrub Oak Oak, Oak (1) 100% 2A Chaparral San Juan Mixed Coast Live 2.67 Creek 7 1 0.09 1-10% 76-100% 0% 0 Chaparral Oak (6) Trib 3

San Mateo Cottonwood 1.83 8 Oak 8 1.72 1-10% 76-100% 1-10% 0.06 Canyon Willow (6) San Mateo Mixed Coast Live 0, 11-25, Canyon 5 4.8 3 0.19 76-100% 0% 0 Chaparral Oak, Oak 26-50% Trib 11 Coast Live San Mateo Mixed Oak, Oak, Canyon 3 - 1 0.25 1-10% 0% 0% 0 Chaparral Scrub Oak Trib 2 Chaparral Coast Live San Mateo Mixed Oak, 4.6 0, 76- Canyon 6 4 0.41 0% 0% 0 Chaparral Cottonwood (5) 100% Trib 7 Willow San Mateo Mixed Coast Live 9 1-10, 51-75, Canyon 5 5 0.23 0% 0.02 Chaparral Oak (3) 11-25% 76-100% Trib 9 Santa 11-25, Mixed Cottonwood Margarita 17 - 17 0.94 1-10% 26-50% 26-50% 1.4 Chaparral Willow River Tenaja Mixed 6.35 11 Oak 7 0.23 1-10% 0, 51-75% 0% 0 Canyon Chaparral (10) Coast Live Oak, Wildhorse Mixed Cottomwood 6.67 11-25, 4 3 0.3 1-10% 26-50% 1.4 Canyon Chaparral Willow, (3) 26-50% Sycamore- Alder Totals 150 93 (62%) Habitat data for USGS sites (Fuller Mill , Dark Canyon and Hall Canyon tributaries) are not incorporated into these results. *Slope was not collected at every reach. For the tributaries where slope was not collected at every reach, the number of sites were slope was collected is presented in parentheses. ** When there are only two segments per creek, the total range of pools is given. ªThe most frequently represented percentages

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Coast Range Newt (TATO) We detected TATO at 8 stream branches and 25 segments in the Santa Rosa Plateau (Adobe Creek) and the Santa Ana Mountains Bioregion (Wildhorse Canyon, Tenaja Canyon, San Juan, and San Mateo Creeks) (Table 2, Figure 2). Adults, juveniles, and egg masses of TATO were all detected during these stream surveys, with at most 2 egg masses, 7 juveniles, and 78 adults found in any stream segment (Table 4). We observed a total of 373 TATO (all life stages) during the stream surveys in 2007.

Table 4. Coast range newt (TATO) detections in 2007. Note that abundances are estimates. Survey Date Creek Name Segment No. Habitat Location Lifestage* Abundance 29-Mar Adobe Creek 4 Bank JUV 3 29-Mar Adobe Creek 4 Pool ADL 32 30-Mar Adobe Creek 5 Pool ADL 14 05-Apr Adobe Creek 1 Pool ADL 32 05-Apr Adobe Creek 1 Pool JUV 7 05-Apr Adobe Creek 2 Pool ADL 9 06-Apr Adobe Creek 3 Pool, Bank ADL 78 06-Apr Adobe Creek 3 Bank JUV 4 06-Apr Adobe Creek 3 Pool EM 2 20-Apr San Mateo Canyon 55 Pool UNK 1 San Mateo Canyon 24-Apr Tributary 9 6 Pool ADL 45 San Mateo Canyon 24-Apr Tributary 9 6 Pool EM 1 San Mateo Canyon 24-Apr Tributary 9 6 Pool JUV 4 San Mateo Canyon 25-Apr Tributary 9 7 Bank JUV 4 San Mateo Canyon 25-Apr Tributary 9 7 Pool ADL 26 San Mateo Canyon 25-Apr Tributary 9 5 Pool ADL 12 26-Apr Wildhorse Canyon 2 Pool ADL 1 30-Apr Wildhorse Canyon 3 Pool ADL 1 30-Apr Wildhorse Canyon 3 Bank JUV 1 01-May San Juan Creek Trib 2 3 Other JUV 1 San Mateo Canyon 01-May Tributary 9 3 Bank ADL 14 San Mateo Canyon 01-May Tributary 9 4 Bank ADL 19 San Mateo Canyon 01-May Tributary 9 4 Bank JUV 2 San Mateo Canyon 02-May Tributary 11 1 Pool, Bank ADL 1 San Mateo Canyon 02-May Tributary 11 2 Bank ADL 9 San Mateo Canyon 02-May Tributary 11 3 Pool, Bank ADL 1

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Table 4 continued. Survey Date Creek Name Segment No. Habitat Location Lifestage* Abundance 10-May San Mateo Canyon 39 Pool ADL 1 San Mateo Canyon 11-May Tributary 7 5 Pool ADL 1 San Mateo Canyon 11-May Tributary 7 6 Pool ADL 1 11-May Tenaja Canyon 4 Pool ADL 14 11-May Tenaja Canyon 4 Pool EM 2 11-May Tenaja Canyon 6 Pool ADL 1 11-May Tenaja Canyon 5 Pool ADL 14 06-Jun Tenaja Canyon 17 Pool ADL 12 06-Jun Tenaja Canyon 18 Pool JUV 2 TOTAL 8 25 373 *Adult (ADL), Juvenile (JUV), Egg Mass (EM), Unknown (UNK)

Table 5 lists the habitat characteristics where we observed TATO, illustrating that most stream segments at TATO detection locations were surrounded by chaparral upland communities (15 out of 25 sites, 60%) with oak (20%) being the second most dominant upland community type. Nearly half (44%) of all detection locations had riparian communities characterized by oak habitat while the remaining 56% of segments were comprised of either willow habitat (32%) or a variety of other riparian community types (Sycamore-Alder, Mule Fat Scrub, or unknown/other totaled 24%). The water velocity in segments where TATO were detected was ≤ 0.5 m/s in all cases. Additionally, the water depth at the beginning of each segment was less than/ equal to 0.55 m for all segments. Of the segments where TATO were detected, 17 out of 25 (68%) were composed of at least 50% medium pools (Table 5). The wetted lengths of most segments were comprised primarily of medium pools. Shallow pools comprised less than 25% of more than half of all segments (17 of 25) while deep pools comprised less than 25% of most segments (21 of 25) (Table 5). California Red-legged Frog (RAAU) Two of 4 Core Areas were visited for daytime visual surveys. Twenty of the 159 stream segments (5000 m) we surveyed were potentially suitable for RAAU. No RAAU or any evidence of RAAU breeding was detected by Monitoring Program biologists in 2007.

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Table 5. Habitat characteristics at TATO locations. Depth represents the water depth at the start of each segment. Data in columns "Shallow", "Medium", and "Deep" represent portions of segments with pools of this depth and are recorded and presented as a range. Velocity at the start of each segment along which TATO were detected was ≤ 0.5 m/s. Survey Stream Segment Depth Upland Riparian Shallow Medium Deep Date Name No. (m) Community Community Unknown/ Adobe Willow 29-Mar 4 0.4 51-75% 11-25% 1-10% Other Creek Scrub Grassland

Unknown/ Adobe Willow 30-Mar 5 0.45 1-10% 51-75% 51-75% Other Creek Scrub Grassland

Adobe Sycamore- 05-Apr 1 0.13 11-25% 26-50% 26-50% Sage Scrub Creek Alder Adobe Willow Willow 05-Apr 2 0.42 11-25% 51-75% 26-50% Creek Scrub Scrub Adobe Willow Willow 06-Apr 3 0.45 11-25% 51-75% 11-25% Creek Scrub Scrub San Mateo Coast Live 24-Apr Canyon 6 0.44 26-50% 51-75% 0% Oak Oak Trib 9

San Mateo Unknown/ Unknown/ 25-Apr Canyon 7 0.12 1-10% 76-100% 0% Other Other Trib 9 Chaparral Riparian

San Mateo Scrub Oak Willow 25-Apr Canyon 5 0.16 11-25% 26-50% 26-50% Chaparral Scrub Trib 9

Wildhorse Mixed Cottonwood 26-Apr 2 0.55 1-10% 51-75% 11-25% Canyon Chaparral Willow

San Juan Coast Live 01-May 3 0.14 26-50% 26-50% 0% Oak Creek Trib 2 Oak

San Mateo Mixed Willow 20-Apr 55 0.35 1-10% 76-100% 11-25% Canyon Chaparral Scrub

San Mateo Mixed Coast Live 11-May Canyon 5 0.15 0% 76-100% 0% Chaparral Oak Trib 7

San Mateo Mixed Coast Live 11-May Canyon 6 0.07 1-10% 76-100% 0% Chaparral Oak Trib 7 Tenaja Mixed Mule Fat 11-May 6 0.28 1-10% 76-100% 0% Canyon Chaparral Scrub

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Table 5 continued. Survey Stream Segment Depth Upland Riparian Shallow Medium Deep Date Name No. (m) Community Community Unknown/ Tenaja Mixed 11-May 5 0.06 26-50% 26-50% 1-10% Other Canyon Chaparral Woodland Tenaja 06-Jun 17 0.5 1-10% 51-75% 0% Oak Oak Canyon Tenaja 76- 06-Jun 18 0.35 0% 0% Oak Oak Canyon 100% San Mateo Mixed Coast Live 01-May Canyon 3 0.24 11-25% 51-75% 11-25% Chaparral Oak Trib 9

San Mateo Mixed Coast Live 01-May Canyon 4 0.17 1-10% 76-100% 1-10% Chaparral Oak Trib 9

San Mateo Mixed 02-May Canyon 1 0.18 0% 76-100% 0% Oak Chaparral Trib 11

San Mateo Mixed Coast Live 02-May Canyon 2 0.28 11-25% 76-100% 0% Chaparral Oak Trib 11

San Mateo Mixed Coast Live 02-May Canyon 3 0.1 26-50% 51-75% 0% Chaparral Oak Trib 11

San Mateo 76- Cottonwood 10-May 39 2 1-10% 1-10% Oak Canyon 100% Willow

Unknown/ Tenaja Mixed 11-May 4 0.11 26-50% 51-75% 0% Other Canyon Chaparral Riparian

Wildhorse Mixed Sycamore- 30-Apr 3 0.1 11-25% 26-50% 1-10% Canyon Chaparral Alder

Mountain Yellow-legged Frog (RAMU) In collaboration with USGS, we detected RAMU in 5 different tributaries and along 11 stream reaches (Table 2). We observed a total of 385 RAMU of all life stages excluding egg masses. We did not observe any RAMU in Hall Canyon. Of these 11 segments where RAMU were detected, 6 had total wetted lengths less than 50%. Of the 385 RAMU observations, 82% (314 observation) were in stream reaches with wetted lengths greater than 50%, while only 18% (71) of observations were made in reaches with less than 50% wet length (summary data provided by USGS). For more specific data on these RAMU detection locations or USGS surveyed locations outside Western Riverside County contact USGS WERC directly.

Western Riverside County MSHCP 13 Biological Monitoring Program Stream Survey Report 2007

Habitat Conditions We detected exotic species at 4 locations during stream surveys (Table 2). Bullfrogs (Rana catesbeiana) were detected along Los Alamos Canyon, San Mateo Canyon, and San Mateo Canyon Tributary 7 and crayfish (Procambarus clarkii) were observed along San Mateo Canyon and Santa Margarita River (Table 2). The majority of streams surveyed in 2007 (excluding those streams surveyed in collaboration with USGS) were surrounded by upland communities comprised primarily of mixed chaparral (Table 3). The most dominant riparian community types were oak (14 of 24 streams) and willow (8 of 24). Of 160 stream segments, 58% were completely dry. Of the segments containing water at all along the reach, only 4 had average water depths across all surveyed segments of greater than 1 m at the start of each reach. Those streams include: Arroyo Seco (5.13 m), Cole Creek (2.39 m), Los Alamos Canyon Tributary 3 (1.4 m), and San Mateo Canyon (1.72 m). Of the remaining streams, 15 had average initial water depths of less than 0.5 m. Additionally, all but one stream surveyed had an average of low to no flow (<1 m/sec) water velocity. Cole Creek Tributary 6 had an average velocity of 1.75 m/sec from the 2 of 7 wet reaches (Table 3).

DISCUSSION The focus of stream surveys in 2007 was to assess stream habitats in the Conservation Area for suitability for BUCA, TATO, RAAU, and RAMU and to document breeding locations within species-specific Core Areas and other potentially suitable habitat in the Conservation Area. We surveyed a total of 161 stream segments in 2007, representing approximately 40 km of stream habitat. A little more than half (53%) of the segments were in Cleveland National Forest portion of the Santa Ana Mountains (Core Area), over one quarter (28%) were on the Santa Rosa Plateau Core Area. Of the 3 Covered amphibian species targeted in 2007, only TATO and RAMU were detected. We have no clear understanding why we did not detect BUCA in 2007, though at one otherwise suitable location (Los Alamos Canyon), bullfrogs were detected. The Monitoring Program will continue to conduct surveys for the presence/absence of BUCA and RAAU juveniles, tadpoles, and egg masses as part of the initial Inventory Phase. Species objective 5 for TATO requires the Monitoring Program to document that newts are maintaining occupancy of at least 75% of their occupied habitat and to determine if successful reproduction is occurring at known breeding locations within Core Areas and other potentially suitable habitat in accessible areas of the MSHCP Conservation Area. In 2007, TATO were surveyed and detected within both Core Areas (Santa Ana Mountain Bioregion and the Santa Rosa Plateau). Within these Core Areas, TATO were detected at 25 segments of 8 different streams. Survey efforts for TATO were focused on the Cleveland National Forest (a portion of the Santa Ana Mountain Bioregion) and the Santa Rosa Plateau, which accounts for coverage of approximately 60% of the listed MSHCP Core Areas for TATO. As breeding activity in northern portions of the Santa Ana Mountains remains unknown, we cannot currently conclude whether or not the MSHCP species objective stated above was met. The Monitoring Program will attempt to document TATO breeding activity in the northern portions of the Santa Ana Mountains in future years.

Western Riverside County MSHCP 14 Biological Monitoring Program Stream Survey Report 2007

Despite below average precipitation in 2007, we found RAMU at 11 segments in the San Jacinto Mountains. In addition, RAMU were detected in greater numbers in stream segments with greater than 50% wetted length than in segments with less than 50% wetted length (82% of detection), providing further information towards habitat suitability in the San Jacinto Mountains. These data exclude Hall Canyon reaches where habitat data were not available at the time of this report. To fully assess the importance of these data, historic and other current RAMU locations and habitat characteristics will need to be considered. We found exotic species (R. catesbeiana and Procambarus clarkii) in one of the two RAAU Core Area streams we surveyed. We do not have enough data to conclude that RAAU were not located at these sites because these exotic species were present, but this is important to note. RACA adults grow to be very large frogs and are known to prey upon tadpoles (Kiesecker and Blaustein 1997, 1998; Lawler et al. 1999). It has also been shown that RACA tadpoles will prey upon other tadpoles (Kiesecker and Blaustein 1997). These studies confirm that RACA do present a direct threat to the sensitive RAAU species. We continue to characterize habitat along stream segments, including water depth, plant communities and abiotic conditions in the water. These data will be most useful when there is a large enough sample size to statistically determine differences in where aquatic herpetofauna are found. This season only 4 of 67 wet stream lengths (Arroyo Seco, Cole Creek, Los Alamos Canyon Tributary 3 and San Mateo Canyon) had greater than 1 m water depth. Identifying those streams or stream segments that maintain an abundance of water (>1 m) during low precipitation years will also be informative in determining where surveys should be focused in future dry seasons and possibly in identifying stream segments with especially relevant, species specific habitat values. Breeding coast range newts, for example, have been noted to prefer deep pools, slow-moving runs, and riparian and upland habitat characterized as have been grassland, woodland, or forest. Recommendations for Future Surveys Current budget for the 2008 season will allow us to continue to look for populations of TATO, to address Core Area specific objectives for TATO and BUCA, and conduct RAAU nighttime surveys in the last known historic locations. We will continue to survey all the streams within Conservation Areas. We also plan to continue collaboration with USGS to monitor San Jacinto Mountain populations of RAMU. With a budget that allows for more field crew, we would be able to conduct more intensive nighttime surveys for RAAU during the fall/ winter breeding season and complete the habitat assessment surveys for all streams within Conservation Areas in a more timely manner. Once each of the streams within Conservation Areas have been surveyed at least once, a habitat summary can be created for each stream, assessing which segments should be targeted for further surveys of target amphibian species. At that time, monitoring of known TATO and other populations should continue and incorporate analyses of Percent Occupancy and population structure.

Western Riverside County MSHCP 15 Biological Monitoring Program Figure 1. Start locations for stream reaches surveyed in 2007. These points exclude reaches surveyed specifically for Mountain yellow-legged frogs. These data are managed by USGS and were unavailable at the time of this report.

Legend Stream Survey Start Points Highways Lakes Streams µ Date: 12 December 2007 Conservation Area Created By: Natalie K. Marioni UTM Nad 83 Zone 11 Planning Area Boundary 0 5 10 20 30 Km MSHCP Biological Monitoring Program Figure 2. Coast range newt (TATO) and Mountain Yellow Legged Frog (RAMU) detections along stream survey reaches in 2007.

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")")")") ") ") ")")")")") ") ")")") ") ")")")")") Legend )" RAMU Detections )" TATO Detections Stream Survey Start Points Highways Streams Lakes µ Date: 12 December 2007 Conservation Area Created By: Natalie K. Marioni UTM Nad 83 Zone 11 Planning Area Boundary 0 5 10 20 30 Km MSHCP Biological Monitoring Program Stream Survey Report 2007

REFERENCES Dudek & Associates. 2003. Western Riverside County Multiple Species Habitat Conservation Plan (MSHCP). Final MSHCP, Volumes I and II. Prepared for County of Riverside Transportation and Lands Management Agency. Prepared by Dudek & Associates, Inc. Approved June 17, 2003. Kiesecker , J. M. and A. R. Blaustein.1997. Population differences in response of red-legged frogs (Rana aurora) to introduced bullfrogs. Ecology. 78(6):1752-1760. Kiesecker , J. M. and A. R. Blaustein. 1998. Effects of introduced bullfrogs and smallmouth bass on microhabitat use, growth, and survival of native red-legged frogs (Rana aurora). Conservation Biology. 12(4):776-787. Lawler, S. P., D. Dritz, T. Strange, M. Holyoak. 1999. Effects of introduced mosquito fish and bullfrogs on the threatened California red-legged frog. Conservation Biology. 13(3):613- 622. Miller, L. and A.H. Miller. 1936. The northern occurrence of Bufo californicus in California. Copeia: 176. Stebbins, R. C. 1951. Amphibians of western North America. University of California Press, Berkeley and Los Angeles, California. ix – 539 pp. Sweet, S. S. 1989. Observations on the biology and status of the arroyo toad, Bufo microscaphus californicus, with a proposal for additional research. Department of Biological Sciences, University of California, Santa Barbara, California. Unpublished report. 23 pp. Sweet, S. S. 1992. Ecology and status of the arroyo toad (Bufo microscaphus californicus) on the Los Padres National Forest of southern California, with management recommendations. Contract report to United States Department of Agriculture, Forest Service, Los Padres National Forest, Goleta, California. 198 pp. U.S. Geological Survey. 2005. Draft USGS Aquatic species and habitat assessment protocol for southcoast ecoregion rivers, streams, and creeks. Western Ecological Research Center. Sacramento, CA.

Western Riverside County MSHCP 18 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT Appendix A: USGS Stream Survey Protocol

USGS Aquatic Species and Habitat Assessment Protocol for Southcoast Ecoregion Rivers, Streams, and Creeks

Survey Protocol

U.S. DEPARTMENT OF THE INTERIOR

U.S. GEOLOGICAL SURVEY

WESTERN ECOLOGICAL RESEARCH CENTER

Western Riverside County MSHCP 19 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT USGS Aquatic Species and Habitat Assessment Protocol for Southcoast Ecoregion Rivers, Streams, and Creeks

BY CHERYL BREHME1, CYNTHIA J. HITCHCOCK2, ADAM BACKLIN2, SARA COMPTON2, STACIE HATHAWAY1, AND ROBERT FISHER1

U.S. GEOLOGICAL SURVEY WESTERN ECOLOGICAL RESEARCH CENTER

SURVEY PROTOCOL

1San Diego Field Station-Carlsbad Office USGS Western Ecological Research Center 6010 Hidden Valley Road Carlsbad, CA 92009

2San Diego Field Station-San Diego Office USGS Western Ecological Research Center 5745 Kearny Villa Road, Suite M San Diego, CA 92123

Sacramento, California 2005

Western Riverside County MSHCP 20 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT U.S. DEPARTMENT OF THE INTERIOR GALE A. NORTON, SECRETARY

U.S. GEOLOGICAL SURVEY Charles G. Groat, Director

The use of firm, trade, or brand names in this report is for identification purposes only and does not constitute endorsement by the U.S. Geological Survey.

For additional information, contact:

Center Director

Western Ecological Research Center

U.S. Geological Survey

3020 State University Drive, East Modoc Hall

Sacramento, CA 95819

Western Riverside County MSHCP 21 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT TABLE OF CONTENTS 1.0 Introduction...... 1 1.1 Purpose...... 2 2.0 Natural History Notes ...... 2 2.1 Key Characteristics of Natives...... 2 2.2 Key Characteristics of Non-natives ...... 3 3.0 Before Going into the Field ...... 3 3.1 Preparing a Survey Map...... 3 3.2 Predefine the Survey Site Names...... 7 3.3 Field Preparation (at lab or office)...... 9 3.4 Materials ...... 9 3.4.1 Field Kit ...... 9 4.0 Survey Protocol...... 10 4.2 Navigate to Site/Calibrate DO Meter...... 10 4.2 Start of Survey Data...... 10 4.3 Water Quality and Stream Measurements ...... 11 4.4 Search/Survey Techniques...... 13 4.5 Animal Records ...... 14 4.6 Landscape and Vegetation Characterization...... 15 5.0 Post-survey Procedures...... 17 Literature Cited ...... 18 Appendix 1 Additional Information on Landscape and Stream Attributes ...... 22 Appendix. 2 Vegetative Communities List for Riparian and Upland Habitats ...... 28 Appendix 3. Examples of site information formatted into an Excel spreadsheet to submit as predefined survey reaches...... 32 Appendix 4 Instructions for Downloading/Uploading GPS data to/from Garmin Units..33 Appendix 5. Calibration Procedures for YSI 85 (DO/Conductivity), Oakland pHTestr 2, and Oakland ECTestr Low (Conductivity)...... 35 Appendix 6. Photographs of Southcoast-Ecoregion Stream-associated Amphibians ...... 38 Appendix 7. Paper Data Form ...... 41

Western Riverside County MSHCP 22 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT 1.0 INTRODUCTION Global and local declines in native amphibian species are well documented (e.g. Blaustein and Wake 1990; Jennings and Hayes, 1994; Fisher and Shaffer 1996; Stuart et al. 2004). Declines have been attributed to habitat loss, climate change, reductions in water quality, pesticide use, pathogens, human modifications to landscapes and hydrological regimes, and introduction and proliferation of non-native species, among other factors (see reviews Hayes and Jennings, 1986; Wake, 1991; Jennings and Hayes, 1994; Blaustein et al., 1997; Morell, 1999; Knapp and Matthews, 2000; Fellers et al., 2001; Kiesecker et al. 2001; Paul and Meyer, 2001; Davidson et al., 2002; Hayes et al., 2002; Kats and Ferrer, 2003). Amphibians may be particularly vulnerable due their physiology and life history traits, with 1856 species (32.5%) threatened with extinction (IUCN 2001, 2003). There is a growing need to investigate the causes of species declines in order to provide the information needed to make effective conservation and management decisions. In response to global and national amphibian declines, in 2000, the President and Congress directed the Department of Interior (DOI) to develop a plan to initiate monitoring of trends in amphibian populations on DOI lands. With a long history in amphibian research, USGS is leading the Amphibian Research and Monitoring Initiative (ARMI) program in cooperation with NPS (National Park Service), FWS (Fish and Wildlife Service), and Bureau of Land Management (BLM). Although the initiative is specific to DOI and other federal lands, it is our goal to provide a framework for incorporating data collected on non-federal lands and to encourage participation from state agencies, educational institutions and non-governmental organizations. There are three levels of research identified; 1) Base level species inventories, 2) Mid-level monitoring (using a spatial and temporal monitoring approach, proportion area occupied (PAO, MacKenzie et al., 2002, 2003)), and 3) Apex studies (more in depth research into mechanisms of decline; including demographic, malformations, disease, contaminant, and other types of studies). For more information on all aspects of ARMI, please see www.armi.usgs.gov. The aquatic survey protocol presented in this document is meant to be used as a general template for all inventories, mid-level monitoring, and apex studies, as appropriate, of aquatic species in rivers, streams, and creeks in the southcoast ecoregion of California.

Currently, aquatic inventory and monitoring surveys are conducted regularly across the ecoregion by a large number of biologists from federal and state agencies, educational institutions, and non-governmental organizations. Survey methods and data collection differ greatly among biologists and across sites. Because of this, we are often unable to establish detection probabilities requiring standard survey techniques, to analyze what factors influence probabilities of detection for various species, or to build predictive or explanatory species models on more than a localized area. Adopting standard measures and basic survey procedures will allow all participants to share and combine data from multiple efforts, and thus, greatly increase the statistical power and area of inference for any target aquatic species. We will also be better able to assess the suitability of habitats for species, to document declines and/or expansions in species distributions, and to identify any broad scale patterns in species spatial distributions as a result of natural and unnatural factors and processes.

Western Riverside County MSHCP 23 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT 1.1 PURPOSE This document details a minimum standard protocol for conducting daytime inventory and monitoring surveys for aquatic species in creek, stream, and river systems in the southcoast ecoregion of the United States. Although the protocol was developed primarily for amphibian larvae, it is also effective for documenting the presence of many aquatic amphibian life stages, turtles, snakes, fish, and other aquatic taxa.

This protocol describes surveys that are to be conducted in 250 meter segments of rivers, streams, and creeks. Surveys should be conducted during the day and at appropriate times of year for amphibian breeding in order to document eggs and larvae (tadpoles). The timing will depend on the goals of the study and the target species. Additional night-time surveys may be triggered based on detections or non-detections of target species with these daytime surveys. To characterize the habitat, both site and survey specific measures are taken. Site specific characteristics include a set of geomorphological and landscape features, such as slope, stream incision, channel and bank substrate, and permanency of water. Survey specific characteristics include measures of water quality, hydrology, aquatic and streamside vegetative growth (including invasive exotic plants), presence of other aquatic species (including invasive exotic animals) and availability of aquatic refugia, basking areas, and pool habitats. We attempted to include a full suite of standard measures that may be used to adequately describe and predict suitable habitat for variety of target amphibian and other aquatic species, including the arroyo toad (Bufo californicus), California red-legged frog (Rana draytonii), mountain yellow-legged frog (Rana muscosa), California newt (Taricha torosa), and Pacific pond turtle (Emys marmorata), as well as many other native and non-native aquatic species. These measures can then be used as covariates in log-linear modeling and other analyses to determine predictive factors for species presence and probability of detection (MacKenzie et al., 2002). 2.0 Natural History Notes In southern California, there are several amphibian species and life stages that may be encountered while conducting a daytime stream survey. Some of the following species are mainly nocturnal, however during breeding they may become diurnal and their larvae are more likely to be encountered during the day. Species include the following native anurans and caudates: California treefrog adults and larvae (Hyla cadaverina), Pacific treefrog adults and larvae (H. regilla), Western toad adults and larvae (Bufo boreas), red-spotted toad adults and larvae (B. punctatus), arroyo toad larvae (B. californicus), spade foot toad larvae (Spea hamondii), red-legged frog adults and larvae (Rana aurora draytonii), California newt or coast range newt adults and larvae (Taricha torosa); and non-natives: bullfrog adults and larvae (Rana catesbeiana), African clawed frog adults and larvae (Xenopus laevis). 2.1 Key Characteristics of Natives California treefrog adults are generally mottled with different shades of gray dorsally, giving them a granite-like appearance. Their larvae are brown dorsally and often have barred tails with gold flecking. Pacific treefrog adults are variable in color and have an obvious dark eye stripe. The larvae are brown or tan dorsally and have eyes that are on the sides of their head compared to California treefrogs which have eyes that are placed more medially. Both treefrog species have obvious toe pads. Western toad adults have an obvious white or cream-colored

Western Riverside County MSHCP 24 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT dorsal stripe. Larvae are uniformly black when newly hatched and gradually obtain a grey or lighter venter as they become larger. Red spotted toad adults generally have red spots. They have round paratoid glands, each about the size of the eye, and pointed snouts. Larvae are black or dark brown dorsally with dark spotting on the dorsal fin. Arroyo toad larvae have a characteristic white spot on each side of the body although it is not always obvious. As they grow larger their venter becomes creamy in color and their dorsum is mottled with frown and sometimes gold flecks. Spade foot toad larvae have eyes that are very close together at the top of the head. They have a squarish body shape. Red-legged frog adults can be brownish to salmon colored dorsally with darker spots and a light venter. They have long legs with fully webbed hind feet and distinct dorsolateral folds. Larvae are brownish dorsally with a light venter and reach large sizes (to about 75 mm; Stebbins, 2003). Coast range newts are orange to brown dorsally with cream or yellow colored venters. Larvae have dark dorsolateral stripes and external gills. (See appendix X for photographs). 2.1 Key Characteristics of Non-Natives Bullfrogs have a fold of skin around a conspicuous eardrum and banded pattern on the legs; they often make a chirping noise (‘eep’) before jumping in the water. They can be greenish to brown dorsally and no not have distinct dorsolateral folds. Adults can grow to very large sizes (up to 200 mm; Stebbins, 2003). Bullfrog larvae are brown dorsally with distinct darker dots. Larvae can reach up to162 cm (Stebbins, 2003). African clawed frog larvae have tentacles and flattened bodies. Their tails have a dramatic taper that ends in a point. (See appendix X for photographs).

3.0 Before Going into the Field The following preparations must be made prior to conducting your survey: 3.1 Preparing a Survey Map Before surveying a stream, you will need to map out your route and divide the survey into 250 m reaches in order to standardize how our data are being collected and analyzed. When possible, divide the 250 m reaches from the mouth of the stream. When working within larger water systems like the Santa Ana River, dividing the 250 m reaches from the mouth would be labor intensive, and therefore impractical. In this situation, the stream should be divided into 250 m segments at the start of your survey. Separate routes should be made for forks, branches, or tributaries off of a main stream channel (Figure 4). Tributaries should be numbered as the number it is off of the mouth of the main stream, when possible. Again, sometimes this is not possible and in this case it should be numbered as the number that it is off of your survey area. This procedure is described using the TOPO!® mapping software version 3.4.3.

Western Riverside County MSHCP 25 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT

Figure 4. Example of forks, branches, and tributaries that require different site names. 1. Open TOPO!® mapping software version 3.4.3 1.a. On the menu bar (across the top) go to “Preferences” 1.a.i. Select “Distance Units” ÖKm 1.a.ii. Do not use m instead of Km, the distances are not calculated accurately and will off-set your mapping. 2. On the menu bar go to “Tool” 2.a. Select “Route” 3. Right click to zoom in on the map (level 5 of 5, 7.5’ Map Series), and use the route tool to trace the length of your survey reach on the map. Always draw your reach from the direction of the mouth of the system working upstream. The forks, branches, and tributaries will start from where it meets with the main stream. 3.a. Using the mouse, right click on the route you’ve drawn 3.a.i. The TOPO!® Route box appears 3.a.i.1. Select “Build Profile” 3.a.i.1.1. The program generates a profile of the route you have drawn with the elevation gain on the y-axis and the distance in km on the x-axis. 4. On the menu bar go to “Tool” 4.a. Select “Waypoint” 4.a.i. Move the waypoint tool over the built profile, a yellow cross-hairs will appear over the profile. 4.b. Using this tool over the profile: 4.b.i. Click on the beginning of your survey section (closest to the mouth of the stream which is usually the most downstream section). 4.b.i.1. Once you click on the profile, at the start of your section, a yellow dot will appear on the actual route on the map (Figure 5a). 4.b.i.2. Move your cursor to that dot and click. This will create a waypoint at that point.

Western Riverside County MSHCP 26 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT 4.b.i.3. The “TOPO! Waypoint Editor” box will appear with the given latitude/longitude at that point and with the default name. 4.b.i.3.1. Delete the default name and add a short prefix for the waypoint names by entering the initials of the site name (e.g., CC for City Creek) followed by the segment number 1 (CC1). Ö OK. 4.b.ii. Continue marking and naming waypoints, using the built profile at 0.25 km increments for the entire survey (Figure 5b). The final map should look similar to the one shown in Figure 3. 4.b.iii. Delete the default name and add a short prefix for the waypoint names by entering the initials of the site name (e.g., CC for City Creek) followed by the segment number 2, 3, 4, etc. Ö OK.

a.

Western Riverside County MSHCP 27 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT b.

Figure 5. Example using the TOPO! ® mapping software version 3.4.3 profile tool to divide the survey into 250 m reaches. a.) Setting up the initial reach (CC1). b.) Setting up the following reach for your survey.

Western Riverside County MSHCP 28 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT

Figure 6. Partial map of City Creek and it’s associated forks and tributaries and their naming conventions. The City Creek reaches 14-18 for the proposed survey begin at those numbers because the stream was divided into 250 m reaches from the mouth of the stream but those reaches are not seen on this map and will not be surveyed. City Creek Tributary 1 is not broken up into 250 m reaches, because it will not be surveyed.

3.2 Predefine the Survey Site Names 1. Before any field surveys are completed, pre-defined site(s) must be established. The steps for describing and submitting pre-defined site(s) are as follows. This information should be formatted into an Excel spreadsheet (Appendix 1). 2. Enter your predefined survey reach information into the Excel predefined template (see Appendix 1). 3. Choose a name that represents the site. Try not to use abbreviations, but the name must be 40 characters or less. a. Block: Name of a river, stream, canyon, and any other body of water with any associated forks, branches, and tributaries that define an area to be surveyed. (e.g. 1) City Creek West Fork Trib 1 (Tributary is abbreviated to keep it down to 40 characters) (e.g. 2) Moro Canyon b. Site: The reach number (250 m segment) (e.g. 1) Reach 1

Western Riverside County MSHCP 29 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT (e.g. 2) Reach 7 4. Acquire information needed for each survey reach: a. LLID Number: CalFish, the California Department of Fish and Game, and the Pacific States Marine Fisheries Commission developed a statewide 1:100k stream-based hydrography for California. From this dataset, LLID’s (Latitude and Longitude ID) were created to serves as a unique identifier of streams. The LLID’s are based on the latitude/longitude at the mouths of the streams. The LLID was created to more accurately share stream information in a uniform way. Contact Carlton Rochester or Liz Gallegos for the LLID number for your streams. Carlton Rochester: [email protected] 858.637.6884 Liz Gallegos: [email protected] 760.931.1101 x229 b. Datum: WGS84 (World Geodetic System 1984) is the terrestrial reference system that we use, as well as, the only accepted datum for the ARMI (Amphibian Research and Monitoring Initiative) database. We will only accept geographic information using the WGS84 datum. (e.g. 1) WGS84 (e.g. 2) WGS84 c. Start/End GPS Coordinates for Reaches: (e.g. 1) Reach 2 City Creek West Fork Trib 1 Start: 34.17577 117.18965 End: 34.17577 117.18676 (e.g. 2) Reach 7 Moro Canyon Start: 35.58184 117.81640 End: 35.57956 117.81718 d. County: (e.g. 1) San Bernardino County (e.g. 2) Orange County e. State: (e.g. 1) California (e.g. 2) California f. Quad Name (optional): U.S.G.S. 7.5’ Topo Map (e.g. 1) Harrison Mountain, CA (e.g. 2) Laguna Beach, CA g. Property Name: The name of the property that encompasses the site (e.g. 1) San Bernardino National Forest

Western Riverside County MSHCP 30 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT (e.g. 2) Crystal Cove State Park h. Land Owner: The owner of the property (e.g. 1) USDA Forest Service (e.g. 2) California State Parks i. Reserve(s): Any reserve associated with the reach (e.g. 1) None applicable (e.g. 2) Nature Reserve of Orange County, Irvine Ranch Reserve, Laguna Coast Wilderness Park 5. Send this Excel file to Carlton Rochester E-mail: [email protected] Office: 858.637.6884

3.3 Field Preparation (at lab or office) 1. Schedule a two-member team to provide increased safety as well as a greater ability to detect aquatic species. Make sure prior approval has been given to survey the days sites. 2. Check all field equipment against equipment list 3. Download start and end coordinates for all survey sites into your GPS unit. (instructions for downloading into Garmin units in Appendix 2) 4. Calibrate pH and conductivity meters (calibration instructions for YSI 85, ECTestr Low, and pHTestr 2 in Appendix 3)

3.4 Materials Prepare or inspect the field kit. Make sure batteries are fresh and there are sufficient extras. Familiarize yourself with the GPS unit. Make sure coordinate system and datum are set appropriately. The datum WGS84 is the most accurate, when downloading data from a GPS, and the coordinates are recorded in decimal degree or hddd.ddddd°. 3.4.1 Field Kit General: 1. Map 2. Compass 3. Flashlight/Headlamp 4. Extra Food 5. Extra Clothes 6. Sunglasses 7. First-Aid Kit 8. Pocket Knife

Western Riverside County MSHCP 31 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT 9. Waterproof Matches 10. Firestarter 11. Water/Filter/Bottles (Gatorade or similar product in powder form) 12. Whistle 13. Insect Repellents 14 Sunburn Screen (and hat) 15. Reflective Blanket 16. Cell Phone

Survey Specific (Nighttime aquatic presence surveys): 1. Copy of protocol 2. TOPO!® mapping software version 3.4.3 3. Maps (TOPO!) with Lat/Long Data 4. Personal Digital Assistant with field forms (optional) 5. Paper field forms 6. Wheat Lamp or Spot Light 7. Garmin 12 xl handheld Global Positioning System (GPS) unit with survey points downloaded (or accompanying list of coordinates) 8. Thermometer (for air & water temp) 9. Digital Camera 10. USGS field key for aquatic species 11. Extra batteries (AA, AAA, D) depending on equipment 12. Ruler (12 inch with metric) 13. Dip net, electroshocker, waterscope, seine, etc., as needed to detect target species 14. Waders/Water shoes 15. Hand lens

4.0 SURVEY PROTOCOL 4.1 Navigate to Site/Calibrate DO Meter Always start downstream and work your way upstream. This prevents debris from being stirred up making it easier to detect animals. Use your GPS unit to navigate the vehicle(s) closest to the beginning of the site by selecting the “GO TO” button for the beginning lat/long for the reach. If you have 2 vehicles, you may want to park one at the end of the last site, so that you can survey some/all assigned sites and return in the second vehicle. At the vehicle, calibrate the dissolved oxygen meter at ambient temperature (Instructions for YSI 85 meter in Appendix). On foot, navigate to the start point of the site. Since the coordinates are typically figured using a topographical mapping program (TOPO!®), you may need to adjust your position, perpendicular to the start coordinate from the channel, so that you are in the middle of the main channel.

Western Riverside County MSHCP 32 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT

4.2 Start of Survey Data 1. At the start of each survey site, start a new “Stream Survey Form”. The data fields at the top of the form relate to where, when, who, why, and how. a. Project Code: Record the project code for which the data is being collected. b. Survey Type: Record that you are conducting a DAY survey. c. Creek Name: The name of the creek or water course must be reported. d. Survey Method: Select all of the survey methods used during the survey. 1.d.i. The options are Visual encounter, seine, dip net, funnel/minnow trap, call survey, and other. e. Date: Document the date on which the survey is being performed. f. Site Name: Enter the name of the 250 meter study site. See Section 7 for site identification and naming. g. Start Time: The time at which survey efforts began must be recorded. h. Site Photo: Yes/No. Indicate where or not a photo was taken of the study site. Photo should be taken facing upstream. i. # photos: If photos were taken of the site, how many? j. End Time: At the end of the survey efforts at the site, record the time. k. Observer1 through Observer 3: Record the names for each person on the survey.

Project Code Survey Type day/night Date Site Photo Observer1 Creek Name Site Name # photos Observer2 Start Time End Time Observer3 Survey Method*: - choose all that apply Visual encounter, seine, dip net, funnel/minnow trap, call survey, other..

2. The next section of the Stream Survey Form includes site location information, along with several additional site descriptors. These variables may be predefined for the survey site. a. Start Lat: Latitude at the start of the survey site. b. Start Long: Longitude at the start of the survey site. c. Start Elev: Elevation at the start of the study site, in meters. d. Datum: Record the coordinate system used to collect these data points. e. End Lat: Latitude at the end of the survey site. f. End Long: Longitude at the end of the site. g. End Elev: Record the elevation at the end of the study site, in meters. h. Drainage: Name the drainage along which the study site is located. i. Slope: Record the general angle of the site. j. Site Length: Report the distance from the start of the survey site to the end. k. Permanency: How transitory is the nature of the water along the study site? The options are Permanent, Semi-permanent, Temporary, or Unknown.

Coordinates: Start Lat End Lat Slope Start Long End Long Site Start Elev End Elev Length Datum Drainage Permanency* Permanent, Semi-permanent, Temporary, Unknown

3. At the start point of each 250 meter survey site, report the general weather conditions. a. Temperature: Measure air temperature and report in degrees Celsius.

Western Riverside County MSHCP 33 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT b. Notes: Any weather related information that is not captured by any other weather data field should be recorded as notes. c. Conditions: Select the general sky conditions. See the last page of the form for the codes. The options are: clear or few clouds, partly cloudy or variable, cloudy or overcast, fog, mist or drizzle, showers or light rain, heavy rain, sleet or hail, snow, and no data. d. Wind Speed: Report the generat wind speed based on the Beauford scale. See the last page of the form for the codes. The options are: <1 mph - calm, smoke rises vertically; 2~3 mph - light air movement, smoke drifts; 4~7 mph - light breeze; 8~12 mph - gentle breeze leaves/small twigs in constant motion, raises dust; 13~18 mph - moderate breeze, small branches move; 19~24 mph - fresh breeze, small trees begin to sway; 25~31mph - strong breeze, large branches move; 32~38 mph - near gale, large trees begin to sway, noticeably difficult to walk; >39 mph - gale and above; and no data.

Weather: Temperature Condition clear or few clouds, partly cloudy or variable, cloudy or overcast, fog, mist or drizzle, showers or light rain, heavy rain, sleet or hail, snow Notes Wind Speed

4.3 Water Quality and Stream Measurements When water is encountered, usually at the start of the survey site, you will measure and record a number of water quality and stream measurements. Before taking measurements, look for any aquatic species within or next to the water. Document the species before recording water quality and stream measurements (see step 23). If an animal species is recorded and the water is affected by the search (i.e. increased turbulence, substrate in water, etc.), take water quality and stream measurements in the unaffected area upstream, if possible. 1. Water Present: Yes/No, is water present along the study site? If yes, then report the rest of the Water Quality Measurements and Stream Measurements. 2. Water Temperature: Take the temperature of the water with a thermometer until reading is stable and record. Immerse the electrode of the pH Testr 2 into the water and stir around a bit. Wait until the reading is stabilized. 3. pH: Record pH. If using ECTestr for conductivity, immerse the probe in the water and wait until the reading is stabilized. 4. Conductivity: Measure and record specific conductivity in microSiemens ( S). (ºC will be flashing on and off- YMI 85). Turn on YSI Model 85 Dissolved Oxygen Meter (or equivalent) and let it finish the self test (1 minute). Remove the probe from the body and put it in the water, swish around a bit. Wait until the temperature reading has stabilized. Press the mode button to move among the measurement types. 5. DO % Saturation: Measure and record Dissolved Oxygen as a %. (For calibration: multiply altitude (m) by 0.033 for 100’s of feet. 6. DO mg/L: Measure and record Dissolved Oxygen in mg/L. Rinse off all probes with DI water and restore. 7. Channel Surface Water Velocity (m/s): Record surface water velocity in meters per second. Put a small stick/branch in water at mid-channel. Time for 2 to10 seconds, depending upon the speed of the water (slow water= 10 seconds/ fast moving water= 2 seconds) and mark the distance moved. If the stick moves a short distance, measure with tape. If stick moves a longer distance, can use rangefinder to determine the distance traveled. It is easy to have the second observer walk and mark the spot traveled (1cm=.01m.). Do this 3 times and record the average of the 3 measurements. Examples: if the stick moved 5 m in 10 seconds, water

Western Riverside County MSHCP 34 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT velocity equals 0.5 m/s (5 / 10). If it moved 5 cm (.05m) in 10 seconds, the velocity equals 0.005 m/s (.05 / 10). 8. Wetted Channel Width: Measure stream width in meters (wetted portion only) by using measuring tape or a rangefinder. If water is braiding, record total width of wetted portion only. (Note: if channel is braiding, add width of wetted braids to figure total stream width). 9. Channel Water Depth: Measure water depth in centimeters at the thalweg (deepest/high flow portion of the main channel). It may be convenient to immerse a stick (or your leg) in the water and then measure the wetted length of the stick with a measuring tape. If water is not wadeable, estimate depth at mid-channel to nearest meter. 10. Number of wetted braids: Record the number of wetted braids or separate streams of water flow. A single moving water channel equals 1. 11. Transparency: Do a visual estimate of water transparency. An easy method is to set a penny in the bottom of the pool. 12. Choose one of the following options: Clear - can see the year on penny clearly in bottom of pool, Moderate/ Translucent - Cannot see year, but can see outline of penny, or Opaque - cannot see year or outline of penny. 13. Notes: Record any relevant or unusual notes pertaining to water.

Start Water Fields: Water Present Y/N Water Temperature pH Conductivity DO % Saturation DO mg/L Channel Surface Water Velocity (m/s) Wetted Channel Width Channel Water Depth Number of wetted braids Transparency Clear, Moderate/Translucent, Opaqu Notes

4.4 Search/Survey Techniques Start slowly walking up the stream channel, either in the water or immediately adjacent to the water. You will be looking for the following things: 1. Aquatic species including all stream associated amphibian eggs, tadpoles, and adults, snakes, newts, fish, crayfish, Asian clams, beavers and beaver sign. See species list for expected species and field guides for proper identification. 2. Non-native vegetation in water or along stream (arundo, tamarix, watercress, mustard, etc.) 3. Use the following techniques to search for aquatic species. a. Visual encounter: Carefully search the water, especially in pools, along shoreline, and near aquatic refugia for eggs, tadpoles, fish and adult amphibians. Floating material can be gently moved back with finger or stick to look underneath. Look ahead often to spot basking turtles and frogs that may leap into water when they spot you are coming. b. Dip Netting: Some fish, tadpoles, and other animals can be found at the edge or in the bottom mud of pooled water, in aquatic vegetation and under ledges along the perimeter of pools. When encountering deep pools and aquatic refugia, first visually check for any aquatic animals, eggs, egg masses. If no eggs are seen, you may take long sweeps with the dip net through these areas. Gently sweep the net along the bottom and sides of the pool or refugia, then check the net for aquatic species by carefully sifting through any

Western Riverside County MSHCP 35 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT muck and debris brought up from the bottom. We recommend using two sizes of nets, a large fish net with a long handle for sweeping deep pools and a small aquarium size net for small fish and tadpoles. Do not disturb any egg masses with dip nets. Capturing tadpoles and fish with a dipnet is also a useful method to observe animals more carefully, take voucher photos, and make positive identifications. Special state and federal permits may be required for handling any listed species. c. Although amphibians are most often heard calling at night. Some can be heard during the day. 4. Also look around every so often (50 meters) and take a mental note of the amount and depth of any pooling water, runs, and riffles, the amount of open channel and banks, the dominant substrate, riparian vegetation and cover in channel and on banks, and amount of potential basking areas and aquatic refugia. This information will be recorded at the end of the reach.

4.5 Animal Records When you first encounter any life stage of an aquatic animal species, record the species and its age class in the animal form. Several additional data fields are included, not all of which are required. 1. Lat/Long: Perform a GPS grab of the first observation within the reach. 2. Species: Record each species/age class combination one time only within the reach. 3. Age: Record the age category of the animals detected. Each age category should be recorded as a separate record. See the last page of the form for the codes. The options are Adult, Juvenile, Metamorph, Larvae, Hatchling, and Egg/EggMass. 4. Sex: Sex is not a required data field as part of this protocol. 5. Length (mm): Length is not a required data field as part of this protocol. 6. Weight (g): Weight is not a required data field as part of this protocol. 7. Recap: The recapture status of an individual is not a required data field as part of this protocol. 8. Tissue: Tissue collection is not a part of this protocol and is not a required field. Collection of any specimens will require permits from land owner, Department of Fish and Game, and Fish and Wildlife Service if the species is listed. 9. ID: Individual identification numbers are not a part of this protocol and are not a required data field. 10. Photo: Take several pictures at different angles (top, bottom, and side) as a photographic voucher of the specimen. Also, if it is an unknown, it may be later identified back at the lab/office. 11. Deformities: Note any abnormalities that may be detected. If additional space is need, continue in the notes field. 12. Location within Habitat: Record the location within the habitat tin which the animal was found. The options are pool, run, riffle, bank, upland, splashzone.

Western Riverside County MSHCP 36 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT 13. Notes: Record any pertinent information that does not fit into one of the other data fields.

Animal: Length Weight Lat./Long Species Age CSex (mm) (g) ID Deformities Recap Tissue Photo 1 2 3 4 5 6 7 8 9 10 Location within Habitat Notes 1 pool, run, riffle, bank, upland, splashzone 2 pool, run, riffle, bank, upland, splashzone 3 pool, run, riffle, bank, upland, splashzone 4 pool, run, riffle, bank, upland, splashzone 5 pool, run, riffle, bank, upland, splashzone 6 pool, run, riffle, bank, upland, splashzone 7 pool, run, riffle, bank, upland, splashzone 8 pool, run, riffle, bank, upland, splashzone 9 pool, run, riffle, bank, upland, splashzone 10 pool, run, riffle, bank, upland, splashzone

4.6 Landscape and Vegetation Characterization At the end of the reach, record information on the landscape, vegetation, cover, stream and water characteristics, and non-native plants. 1. Record any non-native plants observed. a. Plant Species: Document the species of plant detected. See plant field guides for identification and lists of invasive non-native plant species. b. Size Class: For each species report the abundance of that species across the site. d. The options are few plants, scattered small patches, or large contiguous stands. 2. In the Landscape/Vegetation section, report characteristics at a typical location along the site.

Exotic Plants: Plant Species Size Class Plant Species Size Class few plants, scattered small patches, large contiguous stands few plants, scattered small patches, large contiguous stands few plants, scattered small patches, large contiguous stands few plants, scattered small patches, large contiguous stands few plants, scattered small patches, large contiguous stands few plants, scattered small patches, large contiguous stands

a. Channel width/bankful (m): Measure and record the channel width using a measuring tape or rangefinder. See "Definitions" section for definitions of these landscape variables. b. Flood prone width: Measure and record the flood prone width using a measuring tape or rangefinder. See "Definitions" section for definitions of these landscape variables. c. Entrenchment Ratio: Divide the flood plain width by the channel/bankful width to determine the entrenchment ratio. d. Basking areas present: Were basking areas present? Record Yes or No. If Yes, identify the type(s) of basking areas observed within the reach. The options are sunny rocks, open banks, other. Select all that apply. e. % overhead canopy: Estimate the percent of canopy cover estimated at 45°angles over the channel. This would be cover from trees and tall shrubs growing in the channel and

Western Riverside County MSHCP 37 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT on the bank, shading the channel. The options are 0%, 1-10%, 11-25%, 26-50%, 51- 75%, 76-100%. f. Upland Community: Record the dominant vegetation community outside of the main channel. This may be the habitat in the floodplain, terrace, or upland. (See Appendix for a list of vegetation communities). g. Riparian Community: Record the dominant riparian community. (See Appendix for a list of vegetation communities). h. Dominant Riparian Plants: Record the top 3 dominant riparian plant species. i. Bank substrate: Estimate and record the top 3 dominant substrate types on the bank and the relative percentage of each along the entire reach. The choices for substrate are clay, silt, sand, pebbles, cobble, boulders/bedrock, leaf-litter, and fallen logs/trees. See the “Definitions” for descriptions of these categories. The options for percentage are 0%, 1- 10%, 11-25%, 26-50%, 51-75%, 76-100%.

Western Riverside County MSHCP 38 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT

Landscape/Vegetation: Channel width/bankfull (m) Upland Community Flood prone width Entrenchment Ratio Riparian Community (flood plain wdth / bankfull wdth) Basking areas present: Y/N Dominant Riparian Plants (top 3) Choose all that apply: (sunny rocks, open banks, fallen logs, other) Species 1: % overhead canopy 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% Species 2: Species 3: Bank Substrate (Record top 3): pebbles 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% clay 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% cobble 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% dirt 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% boulder/bedrock 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% sand 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% leaf litter 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% gravel 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% fallen logs/sticks 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100%

j. Aquatic Substrate: Estimate and record the top 3 dominant substrate types within the main channel and the relative percentage of each along the entire reach. Choose from clay, silt, sand, pebbles, cobble, boulders/bedrock, leaf-litter, and fallen logs/trees) 3. In the section labeled End Water Fields, estimate and record characteristic of the wetted portion of the site. a. % Wet Length of Survey: Record the percentage of the length of the site containing water, that was not dry. b. % reach with shallow pooling water: Estimate the percentage of the survey reach containing shallow pooling water, less than 10cm deep. c. % reach with medium water: Estimate the percentage of the survey reach containing medium pooling water, greater than 10 cm in depth and less than 1 meter deep. d. % reach with deep pooling water: Estimate the percentage of the survey reach containing deep pooling water which is greater than 1 meter deep. Include side pools, pooling water along side of channel, within main channel, isolated pools when making these estimates. e. % reach with Runs: Estimate the percentage of the survey reach containing runs. See “Definitions” for descriptions of these stream variables. f. % reach with Riffles: Estimate the percentage of the survey reach containing riffles. See “Definitions” for descriptions of these stream variables. g. Plunge pools present: Record whether or not plunge pools were present. Record Yes or No. If Yes, record the estimated number of plunge pools. h. # of plunge pool: Estimate the number of plunge pools that occurred along the site. The options are 1 – 5, 6 – 10, 11 – 20, 21 – 30, 31 – 50, and 51 – 100. i. Aquatic refugia present: Record whether or not aquatic refugia were present along the site. Record Yes or No. If Yes, identify the type(s) of refugia observed within the reach. The options for types of refugia are Undercuts, tree roots, woody debris, rock crevices, aquatic submerged vegetation, emergent veg, and floating material. Select all that apply.

Western Riverside County MSHCP 39 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT

End Water Fields: % Wet Length of Survey 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% % reach with shallow pooling water 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% % reach with medium pooling water 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% % reach with deep pooling water 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% % reach with Runs 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% % reach with Riffles 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% Plunge pools present Y/N # of plunge pool Aquatic refugia present Y/N Choose all that apply: Undercuts, tree roots, woody debris, rock crevices, aquatic submerged vegetation, emergent veg, floating material Aquatic Substrate (Record top 3): pebbles 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% clay 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% cobble 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% silt 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% boulder/bedrock 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% sand 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% leaf litter 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% gravel 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100% fallen logs/sticks 0%, 1-10%, 11-25%, 26-50%, 51-75%, 76-100%

4. The last section of the form documents disturbance and impacts to the site. j. Disturbance Type: Record the nature of the disturbance that was at the study site. k. Intensity of Disturbance: Estimate the level of the disturbance across the site as a whole. The options are Light, Moderate, and Heavy.

Recent Disturbance: Disturbance Type Intensity of Disturbance Light, Moderate, Heavy Light, Moderate, Heavy Light, Moderate, Heavy Light, Moderate, Heavy Light, Moderate, Heavy Light, Moderate, Heavy Light, Moderate, Heavy Light, Moderate, Heavy Light, Moderate, Heavy Light, Moderate, Heavy Light, Moderate, Heavy

5. At the end of the search efforts at the site, enter the end time of the survey, back at the top of the front page. Survey times can be used to calculate search effort and other parameters. 6. Expected Species List: Return to the first page and check appropriate boxes for species detected, surveyed and not detected, and/or not surveyed or not detected.

5.0 Post-survey Procedures 1. Immediately after returning from the field, all equipment coming in contact with water or mud (i.e. boots, dip nets, seine nets, plastic specimen containers) must be thoroughly disinfected in a 16:1 water/bleach mixture to prevent moving pathogens between study sites. 2. Review and QA/QC the data from the days surveys. Correct any mistakes. 3. Enter data into database. 4. Label photographs and send to project lead. 5. Get positive species identifications from experts if needed 6. Make sure pH, conductivity and DO meters are calibrated and properly stored.

Western Riverside County MSHCP 40 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT LITERATURE CITED Blaustein, A. R., Kiesecker, J. M., Chivers, D. P., and Anthony, R. G. 1997. Ambient UV-B radiation causes deformities in amphibian embryos. Proceedings of the National Academy of Science 94:13735-13737. Blaustein, A. R., and D. B. Wake. 1990. Declining Amphibian Populations - a Global Phenomenon. Trends in Ecology & Evolution 5:203-204. Davidson, C., H. B. Shaffer, and M. R. Jennings. 2002. Spatial tests of the pesticide drift, habitat destruction, UV-B, and climate-change hypotheses for California amphibian declines. Conservation Biology 16(6):1588-1601. Fellers, G. M., Green, D. E., and Longcore, J. E. 2001. Oral chytridiomycosis in the mountain yellow-legged frog. Copeia 2001:945-953. Fisher, R. N., and H. B. Shaffer. 1996. The decline of amphibians in California's Great Central Valley. Conservation Biology 10:1387-1397. Fitzpatrick, F. A., I. R Waite, P. J. D’Arconte, M. R. Meador, M. A. Maupin, and M. E. Gurtz. 1998. Revised Methods for Characterizing Stream Habitat in the National Water-Quality Assessment Program, USGS Water-Resources Investigations Report, 98-4052. Harrelson, C.C., Rawlins, C.L., and Potyondy, J.P., 1994. Stream channel referencesites—An illustrated guide to field techniques: U.S. Department of Agriculture, Forest Service, Rocky Mountain Forest and Range Experiment Station, General Technical ReportRM– 245, 61 p. Hayes, T., K. Haston, M. Tsui, A. Hoang, C. Haeffele, and A. Vonk. 2002. Herbicides: Feminization of male frogs in the wild. Nature 419:895-896. Hayes, M. P., and M. R. Jennings. 1986. Decline of ranid frog species in western North America: are bullfrogs (Rana catesbeiana) responsible? Journal of Herpetology 20:490-509. Hupp, C.R., 1986. Upstream variation in bottomland vegetation patterns, northwestern Virginia: Bulletin of the Torrey Botanical Club, v. 113, p. 421–430. Hupp, C.R., and Osterkamp, W.R., 1985. Bottomland vegetation distribution along Passage Creek, Virginia, in relation to fluvial landforms: Ecology, v. 66, p. 670–681. IUCN- The World Conservation Union. 2001. IUCN Red List Categories and Criteria. IUCN, Gland Switzerland. IUCN- The World Conservation Union. 2003. IUCN Red List of Threatened Species. (http://www.redlist.org) Jennings, M. R., and M. P. Hayes. 1994. Decline of native ranid frogs in the desert southwest. Pages 183-211 in P. R. Brown and J. W. Wright, editors. Herpetology of the North American deserts: proceedings of a symposium. Southwestern Herpetologists Society, Van Nuys, California. Kats, L. B., and R. P. Ferrer. 2003. Alien predators and amphibian declines: Review of two decades of science and the transition to conservation. Diversity & Distributions [print] 9:99-110. Kellerhals et al., 1972 (To be updated) Kiesecker, J. M., A. R. Blaustein, and L. K. Belden. 2001. Complex causes of amphibian population declines. Nature 410:681-684. Knapp, R. A., and K. R. Matthews. 2000. Non-native fish introductions and the decline of the mountain yellow-legged frog from within protected areas. Conservation Biology 14:428- 438.

Western Riverside County MSHCP 41 Biological Monitoring Program DRAFT DRAFT DRAFT DRAFT Knox, J.C., 1985. Responses of floods to Holocene climatic change in the upper Mississippi valley: Quaternary Research, v. 23, p. 287–300. Leopold, L.B., Wolman, M.G., and Miller, J.P., 1964. Fluvial processes in geomorphology: San Francisco, W.H. Freeman, 522 p. MacKenzie, D. I., J. D. Nichols, G. B. Lachman, S. Droege, J. A. Rooyle and C. A. Langtimm. 2002. Estimating site occupancy when detection probabilities are less than one. Ecology 83(8):2248-2255. MacKenzie, D. I., J. D. Nichols, J. E. Hines, M. G. Knutson, and A. B. Franklin. 2003. Estimating site occupancy, colonization, and local extinction when a species is detected imperfectly. Ecology 84(8):2200-2207. Morell, V. 1999. Are pathogens felling frogs? Science 284:728-732. Paul, M. J., and J. L. Meyer 2001. Streams in the urban landscape. Annual Review of Ecology and Systematics 32:333-365. Ritter, D.F., 1978. Process geomorphology: Dubuque, Iowa, Wm. C. Brown, 603 p. Rosgen, D.L. 1994. A classification of Natural Rivers. Catena 22:169-199 Schumm, S. A. 1960. The shape of alluvial channels in relation to sediment type: U.S. Geological Survey Professional Paper 352–B, 30 p. Stuart, S. N., Chanson, J. S., Cox, N. A., Young, B. E., Rodrigues, A. S. L., Fischman, D. L., and R. W. Waller. 2004. Status and Trends of Amphibian Decline and extinctions worldwide. Science 306 (3):1783-6 Wake, D. B. 1991. Declining amphibian populations. Science 253:860. Williams, G.P., 1978. Bank-full discharge of rivers: Water Resources Research, v. 14, no. 6, p. 1141–1154. Wolman, M.G., and Leopold, L.B., 1957. River flood plains—Some observations on their formation: U.S. Geological Survey Professional Paper 282–C, p. 87–109. Wolman, M.G., and Miller, J.P., 1960. Magnitude and frequency of forces in geomorphic processes: Journal of Geology, v. 68, p. 54–57.

Western Riverside County MSHCP 42 Biological Monitoring Program

Appendix B: Monitoring Program hardcopy datasheets

Western Riverside County MSHCP 43 Biological Monitoring Program

Western Riverside County MSHCP 44 Biological Monitoring Program