Lower Creek Oct 6-8, (22)

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1 Gila chub Monitoring in Cienega Creek in 2005, 2007, and 2008 with notes on Gila Topminnow, Longfin Dace, Sonora Mud Turtle, and Huachuca Water Umbel Suzy Ehret, AGFD Fish Specialist-Tucson Regional Office Jeff Simms, BLM Fisheries Biologist-Tucson Field Office Introduction Cienega Creek is one of the last natural aquatic habitats in Arizona supporting an intact native fish fauna which is uncontaminated by exotic fish. It drains portions of the Canelo Hills, Whetstone, Empire, and Santa Rita Mountains in S.E. Arizona and flows northwest into the Tucson Basin where becomes the Pantano Wash. The Pantano Wash and Tanque Verde Creek meet and form the now dry Rillito River, which ultimately flows into the Santa Cruz River. Gila chub have been found in 2 distinct reaches of Cienega Creek separated by 4 miles of dry streambed (Map 1). The upper segment is 1.7 miles long with base flows less than 0.15 cfs or 60 gpm. Aquatic habitats are dominated by pool and thickly vegetated marsh and willow swamp macrohabitat types with a mud substrate. The lower creek is 4.2 miles long and has a monthly mean of 0.25 cfs in June to 1.0 cfs in January and February (USGS 2009). The watershed drains 198 mi² above the USGS gage with annual peak flows that range from 165 cfs to 4,720 cfs during the summer months (USGS 2007 and USGS 2009). Common aquatic habitat associations on Cienega Creek are deep, vertical walled, slit-like pools connected by narrow, swift runs surrounded by several feet of marsh on both sides. Riffles with gravel or cobble substrate are present but uncommon. Stream gradient on Cienega Creek varies but is generally about 0.5%. Aquatic habitats are bordered by Gooding willow, cottonwood, ash and other riparian trees. The broad flood plains and banks are comprised of fine textured alluvium (silt, sand, and clay).marsh adapted plants such as water penny, beggers tick, rushes, deer grass (Hydrocotyle ranunculoides,bidens sp., Juncus sp. and Eleocharis sp, Muhlenbergia repens, ) are common along the creek. and large stands of sacaton (Sporobolus sp.) grass are common on the flood plains. Three native fish species occur in Cienega Creek: Gila chub (Gila intermedia), Gila topminnow (Poeciliopsis o. occidentalis), and longfin dace (Agosia chrysogaster). Fish surveys have been conducted on Cienega Creek since A visual fish count of Gila Chub (Gila intermedia) was conducted in 1990 and spot-checking of chub with electrofishing gear had been conducted. This species was proposed for listing in 2002 and was formally listed as endangered (USFWS 2005). The Bureau of Land Management (BLM) and Arizona Game and Fish Department (AGFD) personnel did a population estimate of Gila chub in 2005 (Foster & Simms 2005). Annual fish surveys have been conducted to follow fish population trends and screen for exotic fishes (Young 1995). This report summarizes results for 2005, 2007, and 2008 fish sampling. Methods Habitat Sampling The smallest pools were defined as a small depression with standing water as found in a marsh or floodplain (Armentrout 1998). Pools were distinguished from glides (wide, shallow habitat) by the lack of or near lack of discernible flow. Cienega Creek has a large variety of pool types including trench-pools, which are typically deep (1-5 ft) and are located in the center of the

2 channel much like a straight pool as decribed by Armentrout (1998). The maximum depth of every pool encountered was measured using a surveyor s rod to the nearest 0.1 foot (3 cm). A waypoint was taken (WGS 83 datum) with a GPS at each pool. Pools where hoop nets were to be set were randomly selected using a random numbers generator. A digital photo was taken, facing upstream, at each pool where a hoop net was set. Dissolved oxygen content was measured with a Yellow Springs Instrument model 550A DO meter at one location at the beginning of each segment, each day. Conductivity was measured with an ExTech II ph/conductivity probe. All water quality instruments were calibrated at least once each day. ph was measured using colorphast indicator strips. Because portions of upper Cienega Creek are known to be anoxic, dissolved oxygen (DO) was measured at every pool in that reach. Nets were set in pools with DO content equal to or greater than 2.0 mg/l to avoid fish mortality and conserve time fishing in locations with little potential. No fish were visible in pools with low DO. Previous efforts to catch fish in these pools revealed a lack of occupancy and large numbers of aquatic insects that can tolerate low dissolved oygen levels. Flow in upper Cienega Creek was determined using a Parshall Flume on October 22, Flows in the lower portion of the creek are measured by a USGS gage station. Fish Sampling All fish were collected using identical, 4.5 foot long, double-throat hoop nets that were 20-inches in diameter supported by four hoops and strung with 1/8-inch mesh netting. All hoop nets had been treated at the factory with a green dip to increase durability and to camouflage placement. In 2005 two poles with attached stretch cords were fitted to each net to ensure that they remained open and fishing when in the water. In other years the nets were stretched open with rope attached at both ends. The hoop net traps were baited using perforated containers filled with Purina Aquamax Carnivore pellets in In all other years nets were baited with dry dog food (Pedigree brand). Traps were set so that a portion of the net was always above water to reduce the likelihood of mud turtle by-catch mortalities. The preferred hoop net set was horizontal but when shorelines were shear then the nets were fished vertically. The number of hoop nets set in 2005 was one net for every thirty feet of pool in order to increase catch for population estimates. Only one net per pool was set in the following years to measure catch rate. Pools were randomly selected for sampling from those meeting the two-foot minimum depth requirement for effective hoop net sets. In 2008, the habitat suitability was also limited to those pools with adequate dissolved oxygen (>2 ppm) in the upper reach. Table 1. Fish sampling dates and number of pools sampled in upper and lower Cienega Creek. In 2005 more than one net was deployed for larger pools in order to maximize catch for population estimates. The upper reach has a large number of pools with low dissolved oxygen, limiting suitable habitat. Reach Survey Time Span No. Available Pools (>2 deep) Upper Creek Oct 26-28, (22) Upper Creek April 30- May 1, (8) Upper Creek Oct 14 Oct 23, (8) Lower Creek Oct 6-8, (22) No. Pools Sampled (number of nets)

3 Lower Creek Oct 10-23, (17) Lower Creek Oct Nov. 13, (20) Mattie Canyon Nov. 20, 2007 Unknown 6 (6) Mattie Canyon Nov , (5) Nets were set on the first day and collected at approximately the same time the next day (± 2 hr). In 2005, fish were fin clipped and returned to the location where collected. Hoop nets were again set, with fresh bait, to gain an estimate of recapture rates. Fish captured in hoop nets were identified, measured (total length) and counted. Catch per unit effort (CPUE) was calculated by dividing the number of fish per species caught by the duration of the trap set in days. The mean, median, standard deviation, and standard error were calculated using MS Excel. Population estimates for individual pools was calculated using a simple Lincoln-Peterson index in both the upper and lower reaches. The formula used is N=M C/R, where N = Population abundance estimator, M = number of individuals originally fin clipped, C = number of individuals collected on day 2, and R = number of day two individuals with a clipped fin (# of recaptures). The Peterson estimator assumes that losses and additions due to emigration, immigration, mortality, and recruitment are zero (closed population). This assumption for Gila chub in Cienega Creek is supported by chub movement activity reported in Shultz and Bonar (2006). All fish were identified and counted. The total lengths (mm) of the majority of Gila chub captured were measured. Gila chub were classified into two age classes: juveniles ( <75 mm) and adults (>75 mm) (Shultz and Bonar 2006). Longfin dace were classified similarly with the cut off being 45 mm (W.L. Minckley, personal communication). Results Habitat Conductivity, ph, and temperature were normal throughout the lower reach of Cienega Creek in 2005, 2007 and Water quality has been compromised by low base flows (stagnation) and excess detritus from a robust riparian plant community in the upper segment of Cienega Creek. In 2008, pools numbered 1-10 had a dissolved oxygen content less than 2.0 mg/l. Pools numbered had DO content equal to or greater than 2.2 mg/l with the majority pools having DO content between 3.0 and 4.0 mg/l. Gila chub and topminnow were captured in a pool with a DO as low as 2.2 mg/l. Flow was taken at the headwaters on 10/22/08 at the same location as the other measurements. We recorded 86.6 gpm for the flow. Table 2. Water measurements in Cienega Creek and Mattie Canyon. Date Time Easting Northing Segment Temperature C ph Conductivity DO (mg/l) 11/9/ No data No data Mattie Canyon /15/ Headwatersbend /14/ Cold Water Spring

4 10/16/ /21/ /22/ /12/ /12/ Falls to Fresno Canyon Headwatersbend ?? Headwatersbend Fresno Canyon to Apache Canyon Mattie Canyon Fish Sampling In autumn 2008, a total of fish 1,345 were captured of which 579 fish were captured in upper Cienega Creek and 766 fish were captured in lower Cienega Creek (Tables 3 and 4). A total of 514 fish were captured in Mattie Canyon in In spring of 2008 a total of 280 fish were captured in upper Cienega Creek. A total of 407 fish were captured in lower Cienega Creek in autumn of In Mattie Canyon, 641 fish were captured in autumn of During the Gila chub population estimate investigation in autumn 2005, a total of 1,453 fish were caught of which 1,078 fish were caught in lower Cienega Creek and 375 fish were caught in the upper reach (Foster & Simms 2005). In the lower reach a total of 808 fish were caught in the initial capture event of the mark/recapture population estimate. In the upper reach a total of 157 fish were caught in the initial capture event during the population estimate. Table 3. Percent species composition and counts in upper Cienega Creek Season/Year Gila chub % (n) Gila topminnow % (n) longfin dace %(n) Autumn 2005* 78 (122) 22 (35) 0 (0) Spring (132) 51 (142) 2 (6) Autumn (136) 77 (443) 0 (0) *Numbers are from initial capture event from mark/recapture data Table 4. Percent species composition and counts in lower Cienega Creek Season/Year Gila chub % (n) Gila topminnow % (n) longfin dace %(n) Autumn 2005* 42 (339) 42 (336) 16 (133) Autumn (247) 26 (106) 13 (54) Autumn (335) 22 (167) 34 (264) *Numbers are from initial capture event from mark/recapture data Table 5. Percent species composition and counts in Mattie Canyon, tributary to Cienega Creek Season/Year Gila chub % (n) Gila topminnow % (n) longfin dace %(n) Autumn (32) 0 (1) 95 (608) Autumn (6) 0 (0) 99 (508) Longfin dace were caught in the upper reach of Cienega Creek only in the spring of Gila topminnows were more abundantly caught in upper Cienega Creek than in lower Cienega Creek in Whereas in 2005, more Gila topminnows were captured in lower Cienega Creek. Higher

5 Frequency (%) numbers of chub continue to be captured in lower Cienega Creek compared to upper Cienega Creek. Of the 514 fish captured in Mattie Canyon in 2008, 508 fish were longfin dace and 6 fish were Gila chub. No Gila topminnows were captured. One Gila topminnow, 32 chub, and 547 longfin dace were captured in 2007 in Mattie Canyon. No nonnative fish, crayfish or frogs were observed or captured during the entire study period. Table 6. Ratio of adults to juveniles AGCH. Date Reach Adult Juvenile Total Oct 10-23, 2007 Lower Cienega Creek Oct Nov. 13, 2008 Lower Cienega Creek April 30- May 1, 2008 Upper Cienega Creek Nov. 20, 2007 Mattie Canyon Nov , 2008 Mattie Canyon Figure 1. Gila Chub Length Frequencies in Lower Cienega Creek in Autumn 2005, 2007, & Fall 2005 Fall 2007 Fall 2008 Length (mm)

6 Frequency (%) Figure 2. Gila Chub Length Frequencies in Upper Cienega Creek in Autumn 2005, Fall 2005 Fall 2008 Length (mm)

7 Feb-05 Sep-05 Mar-06 Oct-06 Apr-07 Nov-07 Jun-08 Dec-08 Jul-09 Average CPUE Feb-05 Sep-05 Mar-06 Oct-06 Apr-07 Nov-07 Jun-08 Dec-08 Jul-09 Average CPUE There was substantial variability in CPUE for all three fish species in all years in LCC, UCC, and MC (Figures 4-9). The mean CPUE and standard error (SE) for GIIN in Mattie Canyon in 2007 was 5.15±3.81 (not shown). In 2008, CPUE ranged from 0 to 252 Gila chub, 0 to 297 Gila topminnow, and 0 to 209 longfin dace for a 1-day set. In most cases the standard deviation was greater than the mean. The mean was normally greater than the median for each species indicating the distribution of CPUE is skewed to the right. Non-parametric tests would have to be used to determine confidence in relative abundance numbers. Figure 4. Average CPUE and SE for GIIN in Lower Cienega Creek Month Figure 5. Average CPUE and SE for POOC in Lower Cienega Creek Month

8 Feb-05 Sep-05 Mar-06 Oct-06 Apr-07 Nov-07 Jun-08 Dec-08 AVerage CPUE Feb-05 Sep-05 Mar-06 Oct-06 Apr-07 Nov-07 Jun-08 Dec-08 Jul-09 Average CPUE Figure 6. Average CPUE and SE for AGCH in Lower Cienega Creek Month Figure 7. Average CPUE and SE for GIIN in Upper Cienega Creek Month

9 Average CPUE Average CPUE Figure 8. Average CPUE and SE for POOC in Upper Cienega Creek Feb-05 Sep-05 Mar-06 Oct-06 Apr-07 Nov-07 Jun-08 Dec-08 Month Figure 9. Average CPUE and SE for AGCH in Mattie Canyon Sep-07 Nov-07 Jan-08 Feb-08 Apr-08 Jun-08 Jul-08 Sep-08 Oct-08 Dec-08 Month Sonora mud turtles were encountered during fish surveys (Table 7). In 2007, leopard frogs were observed at the mouth of Fresno Canyon. A subsequent search by herpetologists (David Kahr, UA) reported that they were lowland leopard frogs. Table 7. Numbers of Sonora mud turtles captured in the Cienega Creek watershed during Gila chub monitoring. Reach Date #KISO Lower Cienega Creek Oct. 14-Nov. 13, Upper Cienega Creek Oct , Upper Cienega Creek April 30-May 1, Lower Cienega Creek Oct , Upper Cienega Creek Oct , * Lower Cienega Creek Oct. 6-8, *

10 Mattie Canyon Nov. 20, *During the Gila chub population estimate. It is unknown if any of these were recaptures. Table 8 gives the locations of Huachuca Water Umbel seen during the fish monitoring accomplished in autumn All locations are in the lower Cienega Creek reach. Table 8. Localities for Huachuca Water Umbel. Easting Northing Discussion Upper Cienega Creek is composed of large deep pools connected by short shallow reaches of flow through thick marsh. Flow within the upper creek is very low; the maximum was achieved half way through the reach and was 0.2 cfs. Other areas are stagnant or flowing only a few gpm. Low flow in combination with detritus from the riparian gallery, especially in the upper reaches likely explains the low dissolved oxygen content. The lower reach of Cienega Creek is composed of glides/runs, riffles, and pools. The flow rate is higher in lower Cienega Creek than in upper Cienega Creek. Simms noted that more sedimentation within lower Cienega Creek had occurred between the 2007 and 2008 sampling events. The number of pools identified has declined since The significance of this decline is likely to have resulted in a decrease in suitable habitat for chub. Bonar and Shultz (2006) found that Gila chub occupied pools and had high levels of site fidelity. A grade control structure in Mattie Canyon failed in This caused increased sedimentation to Mattie Canyon from thousands of cubic yards of stored material. Sediment from Mattie Canyon is being carried downstream into lower Cienega Creek during periods of high flow. Most of Mattie Canyon is composed of glides/runs and riffles with few pools. Many of the pools are shallow. This may explain why not many chub or topminnows have been captured there. The other locations of high sediment load were at Wood Canyon, Pump Canyon and other smaller tributaries. The watershed in these areas is still adjusting to past incision that is nearly a century old and more recent ground disturbance on the watershed. In addition it is worth noting that Cienega Creek just above Fresno Canyon to the Narrows does not flow from June until July/August when the monsoon rains refreshes the shallow aquifer that feeds stream flow (1.2 miles). Reproduction in Gila chub and longfin dace is occurring based on the length data for chub and the age class breakdown for longfin dace. The length data of Gila chub suggests recruitment and shows that annual reproduction has been reported since monitoring began in 2005; however, more sampling sets occurring at the same time period from year to year are needed to detect recruitment and establish a trend in relative abundance over time. In any case, trend estimates are confounded by high levels of variance, but can be used to show the dramatic increases or declines in chub populations through catch rates using comparable techniques.

11 The trend in relative abundance data is inconclusive at this point for the same reasons stated above. Because the capture data did not have a normal distribution, non-parametric tests need to be used to determine the confidence intervals. The 2005 Gila chub population estimate for lower Cienega Creek using the Petersen method was 4, 810 with 334 marked chub of which 32 were recaptured (Foster & Simms 2005). A confidence interval was not given for this estimate. In addition catch rates and numbers of Gila topminnow indicate that this species is still present in large numbers but is relatively localized. Habitat changes from sedimentation have converted large numbers of pools to glides from Wood Canyon to the bedrock falls below Pump Canyon (0.8 miles) and from Mattie Canyon downstream (0.4 miles). Few chub were collected in these reach as nets could not be set in the shallow water in the few remaining pools. No larger fish (chub) were observed in this area as in areas with pools located upstream of the sedimentation. Bodner, Simms and Gori (2007) analyzed 16 years of Gila topminnow capture data. They determined that the Gila topminnow population in Cienega Creek had undergone a significant decline. The topminnow were suspected to have declined from a variety of factors that include poor flows related to the drought (head waters reach), shading, and change in trophic structure from green algae based to diatom and leaf litter based. The switch in trophic structure is wide spread in the upper and lower reaches but not complete due to variation in tree establishment and canopy cover. It is unknown how these factors have impacted Gila chub populations because baseline data before 2005 are lacking. Few leopard frogs, tadpoles or bullfrogs have been encountered during 3 years of survey work with hoop nets, indicating that they are uncommon. The population of Chiricahua leopard frog and lowland leopard frog do not appear to be rebounding from a population crash in the mid 1990 s. Mud turtle numbers appear to be lower in 2008 than past years (unpublished data BLM/University of Arizona). This species is especially easy to trap in baited hoop nets left overnight. Future monitoring will help determine the status of this species which has been common on Cienega Creek historically. The Huachuca water umbel has proliferated since the National Conservation Area was established in The survey of aquatic animals for this project was not specifically focused on the umbel, yet four populations were encountered. The umbel appears to be increasing its distribution and population numbers (patches), based on observation. The head water reach also has water umbel populations discovered while conducting other types of surveys. Huachuca water umbel monitoring should be conducted in the future to better determine distribution and quantify status at LSNCA. Nonnative fishes, crayfish and habitat loss pose a serious threat to desert native fishes (Minckley and Marsh 2009). The fact that no nonnative aquatic species were discovered indicates that the largest potential threat to the aquatic fauna of Cienega Creek is not a concern at this time. Proliferation of ranchettes, and associated ponds, will likely increase the threat of contamination through the transfer of fish and bullfrogs through flood flows in tributaries that

12 connect these ponds to the creek on periodic basis. Other threats continue to be wells associated with development and drought conditions. Literature Cited Armantrout, N.B. compiler Glossery of aquatic habitat inventory terminology. American Fisheries Society, Bethesda, Maryland. Bodner, G., J. Simms, and D. Gori State of the Las Cienegas National Conservation Area: Gila Topminnow population status and trends The Nature Conservancy, Tucson, AZ. Bonar, S.A. and A.A. Schultz Selected aspects of the natural history of Gila chub: final report to the Bureau of Land Mangement. AZ Cooperative fish and wildlife unit, U.S. Geologic Survey, University of AZ, Tucson. Fisheries research report Foster, D. K. and Jeff Simms DRAFT Cienega Creek Fish Surveys 2005 Gila Chub, Gila intermedia, status Investigation. Draft report to the U.S. Bureau of Land Management. Arizona Game and Fish Department, Field Operations Tucson, AZ. Mincley, W.L., and P.C. Marsh Inland fishes of the greater southwest: chronicle of a vanishing biota. University of Arizona Press, Tucson. Shultz, A.A. and S.A. Bonar Selected aspects of the natural history of Gila chub. Final report to the Bureau of Land Management. Arizona Cooperative Fish and Wildlife Unit, U.S. Geological Survey, University of Arizona, Tucson, AZ. Young, K.L., and M.A. Lopez Fall Fish count summary Technical Report 81. Nongame and Endangered Wildlife Program. Arizona Game and Fish Department, Phoenix, AZ. U.S. Fish and Wildlife Service Endangered and threatened wildlife and plants: Listing Gila chub as endangered with critical habitat: final rule. Fed Reg. 70 (211): U.S. Geologic Survey Water-Data report 2007, Cienega Creek near Sonoita, Santa Cruz basin, Rillito subbasin. U.S. Geologic Survey National water information system: web interface. Surface Water Data for Arizona. Surface water monthly statistics for Cienega Creek (gage ) _1= ,00060,1, , &start_dt= &end_dt= &partial_periods=on&format=html_table&date_format=YYYY-MM- DD&rdb_compression=file&submitted_form=parameter_selection_list

13 Map 1. Overview of Cienega Creek.

14 Map 2. Pool locations in the upper end of lower Cienega Creek in autumn Numbers represent waypoints.

15 Map 3. Pool locations in the lower end of lower Cienega Creek in autumn Numbers represent waypoints.

16 Map 4. Pool locations in upper Cienega Creek in autumn Numbers represent waypoints.

17 Table 9. Lower Cienega Creek pool locations in Autumn Random Sample Pool # Waypoint # Easting Northing Maximum Depth (ft.) Photograph Facing Upstream (Table ) X X X X X X X X X X X X

18 X X X X X X X X Table 10. Upper Cienega Creek pool locations in Autumn Random Sample Pool # Waypoint # Easting Northing Maximum Depth (ft.) Photograph Facing Upstream

19 X X X X X X X X Table 11. Mattie Canyon pool locations in autumn Random Sample Pool # Waypoint # Easting Northing Maximum Depth (ft.) Photograph Facing Upstream X X X X X

20 Table 12. Photos of Cienega Creek and Mattie Canyon Autumn 2008 Photo 1. Habitat 2 in lower Cienega Photo 2. Habitat 3 in lower Cienega Figure 3. Habitat 11 in lower Cienega Photo 4. Habitat 13 in lower Cienega Photo 5. Habitat 16 in lower Cienega Photo 6. Habitat 17 in lower Cienega

21 Photo 7. Habitat 28 in lower Cienega Photo 8. Habitat 32 in lower Cienega Photo 9. Habitat 33 in lower Cienega Photo 10. Habitat 40 in lower Cienega Photo 11. Habitat 43 in lower Cienega Photo 12. Habitat 47 in lower Cienega

22 Photo 13. Habitat 50 in lower Cienega Photo 14. Habitat 51 in lower Cienega Photo 15. Habitat 55 in lower Cienega Photo 16. Habitat 59 in lower Cienega Photo 17. Habitat 65 in lower Cienega Photo 18. Habitat 70 in lower Cienega

23 Photo 19. Habitat 73 in lower Cienega Photo 20. Habitat 77 in lower Cienega Photo 21. Habitat 13 in upper Cienega Photo 22. Habitat 16 in upper Cienega Photo 23. Habitat 17 in upper Cienega Photo 24. Habitat 22 in upper Cienega

24 Photo 25. Habitat 24 in upper Cienega Photo 26. Habitat 25 in upper Cienega Photo 27. Habitat 28 in upper Cienega Photo 28. Habitat 29 in upper Cienega Photo 29. Habitat 7 Mattie Canyon Photo 30. Habitat 8 Mattie Canyon

25 Photo 31. Habitat 11 Mattie Canyon Photo 32. Habitat 13 Mattie Canyon Photo 33. Habitat 16 Mattie Canyon Photo 34. BLM intern, C. Rarik measuring depth