Colorado Pikeminnow and Razorback Sucker Larval Fish Survey in the San Juan River During 2017

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017

FINAL REPORT

Michael A. Farrington1, Robert K. Dudley1, Jennifer L. Kennedy1, Steven P. Platania1 and Gary C. White2

1American Southwest Ichthyological Researchers L.L.C. 800 Encino Place NE Albuquerque, New Mexico 87102-2606 & 2Department of Fish, Wildlife, and Conservation Biology 239 Wagar, Colorado State University, Fort Collins, Colorado 80523-1474

SAN JUAN RIVER BASIN RECOVERY IMPLEMENTATION PROGRAM 28 June 2018

i American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017

INTERIM PROGRESS REPORT (FINAL REPORT)

Submitted to:

United States Bureau of Reclamation and the San Juan River Basin Biology Committee under the authority of the San Juan River Basin Recovery Implementation Program

Prepared by:

Michael A. Farrington1, Robert K. Dudley1, Jennifer L. Kennedy1, Steven P. Platania1 and Gary C. White2

Reporting Dates: 1 October 2016 through 31 September 2017

Contract # GS-10F-0249X

ii American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

TABLE OF CONTENTS LIST OF TABLES...…………………………………………………………………………………………… ...... v LIST OF FIGURES ...... vi EXECUTIVE SUMMARY ...... 1 INTRODUCTION ...... 2 Objectives ...... 3 Study Area ...... 3 METHODS...... 4 RESULTS ...... 8 2017 Summary ...... 8 Colorado Pikeminnow (age-0) ...... 9 2017 Summary ...... 9 Sampling-site density data...... 9 Habitat type and location ...... 9 2017 trip and reach ...... 13 Colorado Pikeminnow (age-1+) ...... 13 Sampling-site density data ...... 13 Razorback Sucker (age-0) ...... 13 2017 Summary ...... 13 Sampling-site density data ...... 19 Habitat type and location ...... 19 2017 trip and reach ...... 19 Common Species Data from the Middle and Lower sections (Long-term dataset) ...... 25 Bluehead Sucker ...... 25 Flannelmouth Sucker ...... 25 Speckled Dace ...... 25 Red Shiner ...... 25 Fathead Minnow ...... 25 Common Carp ...... 31 Channel Catfish ...... 31 2017 Razorback Sucker opercular deformities ...... 31 Monitoring sites ...... 31 Phase I RERI sites ...... 39 Upper section (Farmington reach) summary ...... 39 DISCUSSION ...... 42

iii American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Management implications ...... 43 ACKNOWLEDGEMENTS ...... 44 LITERATURE CITED ...... 45 APPENDIX A (Long-term dataset) ...... 50 APPENDIX B (Newly expanded study area) ...... 59 Response to reviewers’ comments ...... 68

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

LIST OF TABLES

Table 1. General linear models of Colorado Pikeminnow (age-0) mixture-model estimates (delta (δ) and mu (μ)), using sampling-site density data (2003– 2017) and covariates, allowing for random effects (R). Models are ranked by Akaike’s information criterion (AICC) and include the AICC weight (wi) ...... 14

Table 2. General linear models of Razorback Sucker (age-0) mixture-model estimates (delta (δ) and mu (μ)), using sampling-site density data (1999– 2017) and covariates allowing for random effects (R). Models are ranked by Akaike’s information criterion (AICC) and include the AICC weight (wi) ...... 22

Table 3. Species composition and habitat type of the six RERI sites sampled in 2017. Six letter species codes are defined in Table A-6...... 40

Table 4. Species composition of Age-0 and Age-1+ fish collected between river mile 180.6 and 147.9 (Farmington to Shiprock, NM) ...... 41

Appendix A

Table A-1. Summary of larval Colorado Pikeminnow in the San Juan River (1993– 2017) and back-calculated dates of spawning...... 51

Table A-2. Summary of larval and age-0 Razorback Sucker collected during the San Juan River larval fish survey 1998–2017 ...... 52

Table A-3. Locality and description of the 15 monitoring sites designated for habitat persistence ...... 53

Table A-4. Summary of age-0 fishes collected in the San Juan River during the 2017 larval fish survey. Effort = 12,358.8 m2...... 54

Table A-5. Summary of age-1+ fishes collected in the San Juan River during the 2017 larval fish survey. Effort = 12,358.8 m2 ...... 55

Table A-6. Scientific names, common names, and species codes of fishes collected in the San Juan River. Asterisk (*) indicates a species was collected in prior surveys but not in the 2017 larval fish survey ...... 56

Table A-7. Covariates used in mixture models for Razorback Sucker ...... 57

Table A-8. Covariates used in mixture models for Colorado Pikeminnow ...... 58

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

LIST OF FIGURES

Figure 1. Map of the 2017 study area with long-term monitoring sites (pink dots)...... 5

Figure 2. Discharge (cfs) and temperature (oC) in the San Juan River during the 2017 sampling period. Grey vertical bars denote individual collecting trip between Shiprock NM and Clay Hills Crossing UT. Yellow vertical bars denote individual collecting trips between Farmington NM and Shiprock NM...... 10

Figure 3. Map of the 2017 age-0 Colorado Pikeminnow collection localities ...... 11

Figure 4. Back-calculated spawning dates for Colorado Pikeminnow plotted against discharge and water temperature. USGS gage #09379500 Mexican Hat, UT...... 12

Figure 5. Colorado Pikeminnow (age-0) mixture-model estimates (E(x)) using sampling- site density data by year (top graph) and by reach (bottom graph). Solid circles indicate estimates and bars represent 95% confidence intervals. Red diamonds indicate simple estimates of mean densities using the method of moments ...... 13

Figure 6. Colorado Pikeminnow (age-0) mixture-model estimates (E(x)), using sampling- site density data (2003–2017) and habitat covariates, for habitat type (top graph) and location within backwaters and embayments (bottom graph). Solid circles indicate estimates and bars represent 95% confidence intervals ...... 16

Figure 7. Density (fish per 100 m2 of area sampled) of age-0 and age-1+ Colorado Pikeminnow (Ptyluc) and age-0 Razorback Sucker (Xyrtex) by trip (top graph) and reach (bottom graph) during the 2017 survey ...... 17

Figure 8. Colorado Pikeminnow (age-1+) mixture-model estimates (E(x)) using sampling- site density data (2003–2017). Solid circles indicate estimates and bars represent 95% confidence intervals. Red diamonds indicate simple estimates of mean densities using the method of moments ...... 18

Figure 9. Map of the 2017 age-0 Razorback Sucker collection localities ...... 20

Figure 10. Back-calculated spawning dates for Razorback Sucker plotted against discharge and water temperature. USGS gage # 09379500 Mexican Hat, UT...... 21

Figure 11. Razorback Sucker (age-0) mixture-model estimates (E(x)) using sampling- site density data by year (top graph) and by reach (bottom graph). Solid circles indicate estimates and bars represent 95% confidence intervals. Red diamonds indicate simple estimates of mean densities using the method of moments ...... 23

Figure 12. Razorback Sucker (age-0) mixture-model estimates (E(x)), using sampling- site density data (2013–2017) and habitat covariates, for habitat type (top graph) and location within backwaters and embayments (bottom graph). Solid circles indicate estimates and bars represent 95% confidence intervals ...... 24

Figure 13. Bluehead Sucker (age-0) mixture-model estimates (E(x)) using sampling-site density data (2003–2017). Solid circles indicate estimates and bars represent 95% confidence intervals. Red diamonds indicate simple estimates of mean densities using the method of moments ...... 26

vi American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 14. Density (fish per 100 m2 of area sampled) of age-0 Bluehead Sucker (Catdis) and Flannelmouth Sucker (Catlat) by trip (top graph) and reach (bottom graph) during the 2017 survey ...... 27

Figure 15. Flannelmouth Sucker (age-0) mixture-model estimates (E(x)) using sampling- site density data (2003–2017). Solid circles indicate estimates and bars represent 95% confidence intervals. Red diamonds indicate simple estimates of mean densities using the method of moments ...... 28

Figure 16. Speckled Dace (age-0) mixture-model estimates (E(x)) using sampling-site density data (2003–2017). Solid circles indicate estimates and bars represent 95% confidence intervals. Red diamonds indicate simple estimates of mean densities using the method of moments ...... 29

Figure 17. Density (fish per 100 m2 of area sampled) of age-0 small-bodied cyprinids: Red Shiner (Cyplut), Fathead Minnow (Pimpro) and Speckled Dace (Rhiosc) by trip (top graph) and reach (bottom graph) during the 2017 survey ...... 30

Figure 18. Red Shiner (age-0) mixture-model estimates (E(x)) using sampling-site density data (2003–2017). Solid circles indicate estimates and bars represent 95% confidence intervals. Red diamonds indicate simple estimates of mean densities using the method of moments ...... 32

Figure 19. Fathead Minnow (age-0) mixture-model estimates (E(x)) using sampling-site density data (2003–2017). Solid circles indicate estimates and bars represent 95% confidence intervals. Red diamonds indicate simple estimates of mean densities using the method of moments ...... 33

Figure 20. Common Carp (age-0) mixture-model estimates (E(x)) using sampling-site density data (2003–2017). Solid circles indicate estimates and bars represent 95% confidence intervals. Red diamonds indicate simple estimates of mean densities using the method of moments ...... 34

Figure 21. Density (fish per 100 m2 of area sampled) of age-0 Common Carp (Cypcar) and Channel Catfish (Ictpun) by trip (top graph) and reach (bottom graph) during the 2017 survey...... 35

Figure 22. Channel Catfish (age-0) mixture-model estimates (E(x)) using sampling-site density data (2003–2017). Solid circles indicate estimates and bars represent 95% confidence intervals. Red diamonds indicate simple estimates of mean densities using the method of moments ...... 36

Figure 23. Percentage of Razorback Sucker with opercular deformities by year. The number of fish examined is reported in parentheses ...... 37

Figure 24. Mean connectivity of the 15 monitoring sites during the five survey trips denoted by gray bars ...... 38

Appendix A

Figure A-1. Example of field data recorded at each sampling locality ...... 50

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Appendix B

Figure B-1 Densities by reach for Age-0 fish collected in the upper section (Farmington to Shiprock NM). Reach 5 L is the area below Shiprock, Reach 5 U is the area above Shiprock. Species listed are the same (n = 9) as those tracked in the long-term larval fish dataset ...... 59

viii American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

EXECUTIVE SUMMARY

From 16 April to 27 July 2017, five larval fish surveys were conducted between river miles 147.9 (Shiprock, NM) and 2.9 (Clay Hills Crossing, UT) in the San Juan River. From 6 June to 18 August 2017, three additional surveys were conducted between river miles 180.6 (Animas River confluence, Farmington, NM) and 147.9. These additional larval fish surveys were the first to be conducted within this upper section of the San Juan River. During the study period, mean daily discharge was 3,801 cfs (613–8,540 cfs) and water temperature averaged 19.1oC (9.8–27.8oC). Our sampling collections (n = 289) encompassed 12,358.8 m2 of low-velocity habitat. Collections contained 30,227 age-0 and 1,348 age-1+ fish, which represented six families and 16 species. In 2017, we collected age-0 Colorado Pikeminnow (n = 172) between river miles 162.5 and 8.1. Colorado Pikeminnow mesolarvae, metalarvae, and recently transformed juveniles ranged from 9.0 to 22.4 mm (total length). All larval Colorado Pikeminnow were collected between 23 and 27 July. We also collected Colorado Pikeminnow (n = 2) on 16 August downstream of the Piute Farms waterfall. Back- calculated spawning dates spanned a 33-day period from 13 June to 16 July. We also collected 233 age- 1+ Colorado Pikeminnow in 2017. The autumnal abundance of adult Colorado Pikeminnow explained most of the variation in larval fish densities recorded the following summer. The analysis of Colorado Pikeminnow (age-0) sampling-site density data showed that the (δ (Year) μ(Monitoring) model received about half (0.46) of the AICC weight (wi). The estimated densities (E(x)) of age-0 Colorado Pikeminnow in 2017 were significantly higher (P < 0.05) than all preceding years except 2011, 2014 and 2016. Within the habitat types that have contained Colorado Pikeminnow between 2003 and 2017, estimated densities were significantly higher in backwaters (P < 0.05) than in near low velocity and low velocity habitats. There were no differences in estimated densities among spatial sampling locations within backwaters or embayments. Between river miles 155.9 and 5.6, we collected 360 larval Razorback Suckers in 2017. Age-0 Razorback Sucker were collected during each of the five survey trips. Ontogenetic stages ranged from protolarvae to juvenile, and back-calculated spawning dates ranged from 23 March to 9 July. Razorback Sucker spawning in the San Juan River has been documented during each of the last 20 years. There was a negative correlation between May discharge and larval Razorback Sucker abundance. General linear models of Razorback Sucker mixture-model estimates revealed that the (δ(Year) μ(May flow+total stocked)) model received most (0.78) of the AICC weight (wi). The (δ(Year) μ(May flow+monitoring)) and the (δ(Year) μ(May flow+random)) models were the second and third ranked models. These three models, which incorporate the May flow covariate for mu (μ), received 0.97 of the total AICC weight (wi), with estimations of mu (μ) declining with increasing May discharge. Estimated densities of Razorback Sucker were significantly lower (P < 0.05) in 2017 compared to 2002 and 2011– 2016. Within habitats sampled from 1999 to 2017, estimated densities (E(x)) of Razorback Sucker were significantly higher in backwaters (P < 0.05) as compared to all other habitat types. Estimated densities were also significantly lower (P < 0.05) in run habitats compared to all other habitat types. Within backwaters and embayments, there were no significant differences among spatial sampling locations. In 2017, we examined 145 age-0 Razorback Suckers for opercular deformities. While fish were rated for deformities in reaches 4–1 (none collected in Reach 5), deformed fish were only found in reaches 3–1. Deformities were found bilaterally (3.4%, n = 5) and unilaterally (9.0%, n = 13). The overall deformity rate in 2017 (13.1%) was lower than that documented in 2016 (17.6%). During 2017, the 15 monitoring sites were visited 75 times. Overall, monitoring sites were connected to the river 74.7% of the time during 2017. The highest level of connectivity observed was during the April and June surveys, and the lowest occurred during the late-July survey. Monitoring site collections contained 3,334 age-0 fish, including 288 larval Razorback Sucker. We also collected 11 larval and 84 Age-1+ Colorado Pikeminnow from monitoring sites in 2017. Despite high flows in 2017, the phase I RERI sites again provided nursery habitat for larval fishes. Fourteen Age-1+ Colorado Pikeminnow were captured within phase I sites. However, for the first time since the completion of the phase I sites, no larval endangered fishes were collected.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

INTRODUCTION

Colorado Pikeminnow, Ptychocheilus lucius, and Razorback Sucker, Xyrauchen texanus, are endangered cypriniform fishes native to the San Juan River, a large tributary of the Colorado River. The decline of these two species across their native range and in the San Juan River has been attributed to fragmentation by instream barriers, channel simplification and flow modifications resulting in changes to the thermal regime (Platania 1990, Ryden and Pfeifer 1994). In addition, the introduction of nonnative fishes has altered predation dynamics and competition for habitat and resources (Clarkson and Childs, 2000). Colorado Pikeminnow (family Cyprinidae – minnows and carps) was listed as an endangered species by the U.S. Department of the Interior in 1974. This species is endemic to the Colorado River Basin and currently occupies only about 20% of its historic range (Behnke and Benson, 1983; Tyus, 1990), Once abundant and widespread, the majority of the remaining Upper Basin individuals occur in the Green River sub-basin (Holden and Wick, 1982; Bestgen et al., 1998; Osmundson and White, 2009). Colorado Pikeminnow have been absent from the Lower Basin for at least 50 years (Minckley and Deacon, 1968; Minckley, 1973; Moyle, 2002). Early investigations into the reproductive success of Colorado Pikeminnow on the San Juan River, were conducted from 1991 to 2001 using larval drift nets. During that period of passive sampling, only six larval Colorado Pikeminnow were collected (Appendix A, Table A-1). Beginning in 2002, the sampling protocol was switched to active collection of larval fishes using larval seines and a raft to navigate the San Juan River. Using this active approach a total of 1,110 larval Colorado Pikeminnow were collected between 2004 and 2017 (Table A-1). San Juan River larval fish studies have shown that Colorado Pikeminnow typically spawns on the descending limb of the summer hydrograph when water temperatures are between 18ºC and 25 ºC (Farrington et al., 2015 and 2017). Following upstream migrations by adults, larval Colorado Pikeminnow drift down river as a dispersal mechanism that disperses offspring to favorable nursery habitats. This passive movement occurs about five days after hatching, which corresponds with the swim-up period for Colorado Pikeminnow larvae reported by Hamman (1981, 1986). Razorback Sucker (family Catostomidae – suckers) was listed as an endangered species in 1991. Despite being one of three endemic Colorado River Basin catostomids, there are few historical San Juan River records of Razorback Sucker. There are anecdotal reports from the late 1800’s of Razorback Sucker occurring in the Animas River as far upstream as Durango, Colorado (Jordan, 1891), but there are no specimens to substantiate this claim. In 1976, Razorback Sucker was verified in the San Juan River when two adult specimens were collected in an irrigation pond near Bluff, Utah (VTN Consolidated, Inc., and Museum of Northern Arizona, 1978). Larval surveys using the same active sampling methods as that for the larval Colorado Pikeminnow survey began in 1998 on the San Juan River in an attempt to document reproduction of stocked Razorback Sucker. The 1998 survey produced the first documentation of reproduction by stocked Razorback Sucker. Razorback Sucker larvae have been documented every year since 1998 (Table A-2). Back-calculated hatching dates derived from individual Razorback Sucker larvae indicates spawning occurs prior to spring run-off often including the ascending limb of the spring hydrograph, and can persist into early summer (Farrington et al. 2017). Mean water temperatures during this period among all years ranged between 7.7–26.5oC. This minimum, maximum and subsequent range of temperatures at which successful spawning by Razorback Sucker has been documented is outside of the temperature range typically reported for this species (Bozek et al. 1990; Tyus and Karp, 1990; Muth et al. 1998; Bestgen et al. 2011). Spawning of Razorback Sucker coincides with spawning of other native catostomids with adults congregating in riffles with cobble, gravel, and sand substrates. Hybridization between Flannelmouth Sucker and Razorback Sucker has been documented where these two species co-occur (Tyus and Karp, 1990; Douglas and Marsh, 1998). Mortality rates are substantial in the early ontogeny of fishes (Harvey, 1991; Jennings and Philipp, 1994). Food production, competition for food resources, and predation, especially in limited nursery habitats, result in high mortality rates of larval fishes (Houde, 1987). These factors are compounded in modified systems with large numbers of nonnative fishes. For example, nonnative Red Shiner, Cyprinella

2 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018 lutrensis, preys on cypriniform larvae (Brandenburg and Gido, 1999; Bestgen and Beyers, 2006). Red Shiner can compose up to 80% of the ichthyofaunal community in nursery habitats in the San Juan River (Propst et al., 2003; Brandenburg and Farrington, 2010) and may have significant impacts on native fish populations. To mitigate these negative effects, attempts to mimic natural flow regimes in regulated systems are used to maintain cues for activities such as spawning and migration of native fishes, create and maintain nursery habitat for larval fishes, and suppress nonnative fish populations (Poff et al., 1998). Natural flow regimes also favor the downstream displacement or drifting behavior of larval fishes and exploitation of the most advantageous feeding and rearing areas (Muth and Schmulbach, 1984; Pavlov, 1994). In many western river systems, higher spring and early summer flows increase sediment transport and turbidity and have been shown to reduce predation of larvae (Johnson and Hines, 1999). Sediment transport during high spring flows also scours substrates providing critical spawning habitat to native catostomids (Osmundson et al., 2002).

Objectives

This work was conducted as required by the San Juan River Basin Implementation Program (2016) Long Range Plan. The goals and objectives of this specific monitoring project are identified in the aforementioned document and listed below:

4.1.1.1 Develop and revise a Standardized Fish Monitoring Plan to assess presence, status, and trends of Colorado Pikeminnow, Razorback Sucker and fish community.

4.1.1.2 Analyze and evaluate monitoring data and produce Annual Fish Monitoring Reports to ensure that the best sampling design and strategies are employed.

4.1.2.1 Conduct larval fish sampling to determine if reproduction is occurring, locate spawning and nursery areas, and gauge the extent of annual reproduction.

4.1.2.5 Deposit, process, and secure San Juan River fish specimens, field notes, and associated data at an organized permanent repository.

4.1.7.2 Provide annual updates of the rate of opercular deformities found in Razorback Sucker.

4.2.3.2 Document and track trends in the use of specific mesohabitat types by larval Colorado Pikeminnow and Razorback Sucker.

4.2.4.1 Identify principal river reaches and habitats used by various life stages of endangered fish.

4.3.1.6 Monitor TNC’s restoration sites.

4.4.1.1 Document and quantify reproduction, survival, and recruitment.

5.1.1.3 Provide detailed analysis of data collected to determine progress towards endangered species recovery in the San Juan River.

STUDY AREA

The San Juan River is a major tributary of the Colorado River and drains 38,300 mi.2 (99,198 km.2) in Colorado, New Mexico, Utah, and Arizona (Figure 1). The major perennial tributaries to the San Juan River are (from upstream to downstream) Navajo, Piedra, Los Pinos, Animas, La Plata, and Mancos rivers, and McElmo Creek. In addition, there are numerous ephemeral arroyos and washes that contribute relatively little flow annually but input large sediment loads during rain events.

3 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

The San Juan River is currently a 224-mile (360 km) lotic system bounded by two reservoirs (Navajo Reservoir near its head and Lake Powell at its mouth). From Navajo Dam to Lake Powell, the mean gradient of the San Juan River is 10.1 ft./mi, (1.9 m/km) but can be as high as 21.2 ft./mi. (4.0 m/km). Except in canyon-bound reaches, the river is bordered by nonnative salt cedar, Tamarix ramosissima, Russian olive, Elaeagnus angustifolia, native cottonwood, Populus fremontii, and willow, Salix sp. Non-native woody plants dominate nearly all sites and result in heavily stabilized banks. Cottonwood and willow compose a small portion of the riparian vegetation. The characteristic annual flow regime of the San Juan River is typical of rivers in the American Southwest, with large flows during spring snowmelt followed by low summer, autumn, and winter base flows. Convective storm-induced flow spikes frequently punctuate summer and early autumn base flows. Prior to operation of Navajo Dam, about 73% of the total annual San Juan River drainage discharge (based on USGS Gage # 09379500; near Bluff, Utah) occurred during spring runoff (1 March through 31 July). Mean daily peak discharge during spring runoff was 10,400 cfs (range = 3,810 to 33,800 cfs). Although flows resulting from summer and autumn storms contributed a comparatively small volume to the total annual discharge, the magnitude of storm-induced flows exceeded the peak snowmelt discharge in about 30% of the years, occasionally exceeding 40,000 cfs (mean daily discharge). Both the magnitude and frequency of these historically unregulated storm induced flow spikes were greater than those recorded in the Green or upper Colorado rivers. Operation of Navajo Dam altered the annual flow regime of the San Juan River. The natural flow of the Animas River ameliorated some aspects of regulated discharge by augmenting spring discharge. Regulation resulted in reduced magnitude and increased duration of spring runoff in wet years and substantially reduced magnitude and duration of spring flow during dry years. Overall, flow regulation by operation of Navajo Dam has resulted in post-dam peak spring discharge averaging about 50% of pre- dam values. Conversely, post-dam base flow increased over pre-dam base flows. Since 1992, efforts have been made to operate Navajo Dam to mimic a more “natural” annual flow regime.

METHODS

We accessed our river collection localities by using 16' (4.9 m) and 12’ (3.7 m) inflatable rafts that transported our personnel and collecting gear. There were not a predetermined number of collections per river mile or geomorphic reach for this study. Instead, collections were made in as many suitable larval fish habitats as possible within the river reach being sampled. The study area was divided into the three discrete sections listed below:  “Upper Section” between Farmington and Shiprock, NM (RM 180.6–147.9).  “Middle Section” between Shiprock, NM and Sand Island, UT (RM 147.9–76.4)  “Lower Section” between Sand Island and Clay Hills Crossing, UT (RM 76.4–2.9)

The long-term dataset comes from one-week concurrent samples of the middle and lower sections, which were conducted monthly during the spawning season. Five surveys were conducted annually within these two sections. Beginning in 2017, three additional surveys were conducted within the upper section of the study area. These additional surveys were designed to document the upper distribution of larval Colorado Pikeminnow and Razorback Sucker. We determined our sampling dates for the upper section based on the presence and abundance of larval fishes in surveys immediately downstream of Shiprock, NM. We used this flexible yet intensive sampling approach to help ensure that adequate numbers of larval fish were collected to document the presence of rare species in the upper section.

4 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 1. Map of the 2017 study area with long term monitoring sites (pink dots).

5 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Collecting efforts for larval fishes were concentrated in low velocity habitats using a 1 m x 1 m fine mesh (0.8 mm) larval fish seine. Several seine hauls (between two and six) were made through an individual mesohabitat depending on the size of that habitat. Beginning in 2013, fishes collected within an individual mesohabitat were preserved by individual seine haul (as opposed to all fish preserved as a single sample). For each site sampled, the length (in meters) of each seine haul was determined in addition to the number of seine hauls per site. Mesohabitat type, length, maximum and minimum depth, substrate, and turbidity (using a Secchi disk) were recorded in the field data sheet for the particular collecting site (Figure A-1). Water quality measurements (dissolved oxygen, conductivity, specific conductance, pH, salinity, and temperature) were also obtained using a multi-parameter water quality meter. Habitat designations used in this report were developed for the San Juan River Basin Recovery Implementation Program’s (SJRBRIP) monitoring projects (Bliesner et al., 2008). A minimum of one digital photograph was recorded at each collection site. River mile was determined to the nearest tenth of a mile using the 2009 standardized aerial maps produced for the SJRBRIP and used to designate the location of collecting sites. In addition, geographic coordinates were determined at each site with a Garmin Geographic Positioning System (GPS) unit and were recorded in Universal Transverse Mercator (UTM) Zone 12 (NAD27). In instances where coordinates could not be obtained due to poor GPS satellite signal, coordinates were determined in the laboratory using a Geographic Information System based on the recorded river mile. Beginning in 2011, ASIR researchers defined 20 monitoring sites throughout the study area in an attempt to assess persistence of backwater habitats. All but three sites were geomorphically similar and were characterized as lateral washes or canyons, which form backwaters during increased river discharge. In 2012 the two monitoring sites not located in lateral washes or canyons were excluded from analysis. In addition, two sites designated in Reach 5 were also excluded because one was fed by irrigation return water and the other was inaccessible at most discharge levels (Table A-3). Because these sites do not have perennial flow, the only habitat types encountered were either backwaters, or, after river levels have subsided, isolated pools. Due to a change in the physical characteristics, the site at river mile 24.5 (John’s Canyon) was removed from the monitoring site list in 2013. Scour at the mouth of the site has led to the formation of a pool or eddy type habitat, depending on discharge; there was no backwater type habitat encountered in 2013. The 15 remaining monitoring sites were visited in each monthly survey. If suitable nursery habitats had formed in them at the time of visitation they were sampled. If they were dry or isolated, photographs were taken and field notes written detailing condition of the habitat. Conditions of monitoring sites were then related back to discharge at time of visitation. Each of the six River Ecosystem Restoration Initiative (RERI) sites located between river miles 132.2 and 127.2 were also the subject of repeated monthly monitoring. Unlike the monitoring sites, these areas were only sampled if suitable nursery habitat was available. The goal of these collections was to detect the presence of fishes, regardless of age class. If a site could not be effectively sampled (e.g. too deep or swift), photos were taken and no collection was made. All retained specimens were placed in plastic bags (Whirl-Paks) containing a solution of 95% ethyl alcohol (EtOH) and a tag inscribed with a unique alphanumeric code that was also recorded on the field data sheet. Samples were returned to the laboratory where they were sorted and identified to species. Specimens were identified by personnel with expertise in San Juan River Basin larval fish identification. Stereomicroscopes with transmitted light bases and polarized light filters were used to aid in identification of larval individuals. Age-0 specimens were separated from age-1+ specimens using published literature that define growth and development rates for individual species (Auer, 1982; Snyder, 1981; Snyder and Muth, 2004). Both age classes were enumerated, measured (minimum and maximum size [mm standard length] for each species at each site), and cataloged in the Museum of Southwestern Biology (MSB), Division of Fishes at the University of New Mexico (UNM). Results reported in this document pertain primarily to age-0 fishes. Raw numbers of age-0 and age-1+ fishes are presented in Appendix A (Tables A-4 and A-5). Scientific and common names of fishes used in this report follow Page et al. (2013) and six letter codes for species are those adopted by the San Juan River Basin Biology Committee (Table A-6). Total length (TL) and standard length (SL) were measured on all Colorado Pikeminnow and Razorback Sucker to be consistent with information gathered by the San Juan River Basin and Upper Colorado River Basin programs. Within this report, lengths of these species are given as TL. The term young-of-year (YOY) can include both larval and juvenile fishes. It refers to any fish,

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018 regardless of developmental stage, between hatching or parturition and the date (1 January) that they reach age-1 (i.e., YOY = age-0 fish). Larval fish is a specific developmental (morphogenetic) period between the time of hatching and when larval fish transform to juvenile stage. The larval fish terminology used in this report follows conventions established by Snyder (1981). There are three distinct sequential larval developmental stages: protolarva, mesolarva, and metalarva. Fishes in any of these developmental stages are referred to as larvae or larval fishes. Juvenile fishes are those that have progressed beyond the metalarva stage and no longer retain traits characteristic of larval fishes. Juveniles were classified as individuals that 1) had completely absorbed their fin folds, and 2) had developed the full adult complement of rays and spines. Modeling ecological data with multiple zeros can be particularly effective when using mixture models (e.g., combining a binomial distribution with a lognormal distribution) to estimate occurrence and abundance separately (White, 1978; Welsh et al., 1996; Fletcher et al., 2005; Martin et al., 2005). Long- term Razorback Sucker (1999–2017) Colorado Pikeminnow, and ichthyofaunal community (2003–2017) sampling-site density data were analyzed using PROC NLMIXED (SAS, 2016), a numerical optimization procedure, by fitting a mixture model using the methods outlined in White (1978). Logistic regression was used to model the probability a site was occupied, and the lognormal model was used to model the distribution of abundance given that the site was occupied. Models provided four parameter estimates for each year ( = delta; probability of occurrence,  = mu; mean of the lognormal distribution,  = sigma; standard deviation of the lognormal distribution, and E(x) = estimated density). Estimated densities incorporate both the delta and mu model estimations. General linear models were used to incorporate covariates to model ,  and . Covariates considered to model annual sampling-site density data for Razorback Sucker (1999–2017) were year, reach, mean March flow and temperature, mean April flow and temperature, mean May flow and temperature, annual number stocked, cumulative number stocked, and fall monitoring captures (1+ overwinter periods) For example, if 100 individuals were collected during fall 2016 we assumed that these individuals would be available to spawn in spring 2017 (Table A-7). This overwinter criteria helps to ensures that fish captured are sexually mature adults (versus sub-adults) when used as a covariate in any particular model. Covariates considered to model annual sampling-site density data for Colorado Pikeminnow (2003–2017) were year, reach, mean June flow and temperature, mean July flow and temperature, cumulative number stocked, and fall monitoring captures of adults greater than 400 mm TL. The same overwinter criteria applied to Razorback Sucker were used for Colorado Pikeminnow (Table A- 8). To facilitate a valid comparison among years and minimize excessive zeros in the model, months that produced a negligible number of specimens (< 1% of the total) were excluded from further analysis. The months considered for age-0 Razorback Sucker occurred earlier in the year (April through June) compared with the months considered for age-0 Colorado Pikeminnow (July and August). In contrast, stocked age-1+ Colorado Pikeminnow occurred throughout the typical sampling season (April–August) and so those months were included in the analysis for that life stage. Fixed effects models for each 0 1  covariate) with the corresponding link function. These fixed effects assume that variation in the data is explained by the covariate. That is, for , there is no over- dispersion or extra-binomial variation, and for , no extra variation provided beyond the constant  model. Random effects models were also considered for  and μ to provide additional variation around the fitted line where a normally distributed random error with mean zero and non-zero standard deviation is used to explain deviations around the fitted covariate. Adaptive Gaussian quadrature as described in Pinero and Bates (1995) was used to integrate out these random effects in fitting the model. The relative fit of data to various models was assessed using goodness-of-fit statistics (logLike = -2[log-likelihood] and AICC = Akaike’s Information Criterion [Akaike, 1973; Burnham and Anderson, 2002] for finite sample sizes). Lower values of AICC indicate a better fit of the data to the model. Models were ranked by AICC values and included AICC weight (wi). All AIC tables present the top models (5-10) that account for > 99.0% of the AICC weight (wi). Differences among null and alternative models were assessed using a log-likelihood ratio goodness-of-fit test (Zar, 2010). For nested models, an analysis of deviance (ANODEV) was used to determine the proportion of deviance explained by the covariates for both the  and μ models and to assess the significance (P < 0.05) of those values based on an F-test (Skalski et al., 1993).

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Additional samples were taken between 2013 and 2017 to increase the overall sample size and provide supplemental information on habitats (i.e., habitat type, and habitat location). Field sampling efforts occurred in nine habitat types (backwater [BW], cobble shoal [CS], eddy [ED], embayment [EM], pool [PO], pocketwater [PW], run [RU], sand shoal [SS], and slackwater [SW]). Additionally, four categories were assigned to habitat depending on where the sample was taken. Shoreline (SH) indicated all samples taken along the land-water interface, open-water (OP) indicated samples taken away from the shoreline, and mouth (MO) or terminus (TR) indicated samples taken from those locations within a backwater or embayment. Habitat-specific density data (i.e., providing information on habitat type, and habitat location) have only been available since 2013. These data provide information on the specific habitat features used by Razorback Sucker and Colorado Pikeminnow. Habitat-specific density data were also analyzed using PROC NLMIXED (SAS, 2016), using the same methods outlined previously, to assess differences among models. A simplified list of five habitats (BW, EM, RU, LV [combining CS, PW, SS, and SW], and NZV [combining ED and PO]) was used for the purpose of statistical analysis since several habitats shared nearly identical low velocity (LV) or near zero velocity (NZV) conditions. Isolated pool habitats were excluded from analysis since fish densities in confined habitats were not comparable to densities in freely accessible habitats. Similarly, habitats that were dry or not sampled were excluded from further analysis. General linear models were used to incorporate covariates to model , , and . Covariates considered to model habitat-specific density data were year, reach, habitat type, and habitat location. Random effects models were used with the joint binomial and lognormal likelihood to provide random errors for the Site*Year combinations. Bivariate normal errors with mean zero and covariance were assumed for each Site*Year combination. A random error (for all model combinations) was added to the logit of the binomial parameter , and a second random error was added to the log of the μ lognormal parameter. Adaptive Gaussian quadrature as described in Pinheiro and Bates (1995) was used to integrate out these random effects in fitting the model using the SAS NLMIXED procedure. Goodness-of-fit statistics (logLike and AICC) were generated to assess the relative fit of data to various models. Hatching dates were calculated for larval Colorado Pikeminnow using the formula: -76.7105+17.4949(L)-1.0555(L)2+0.0221(L)3 for larvae under 22 mm TL, where L = length (mm TL). For specimens 22–47mm TL the formula A = -26.6421+2.7798L is used. Spawning dates were then calculated by adding five days to the post-hatch ages to account for incubation time at 20–22oC (Nesler et al., 1988). Hatch dates of Razorback Sucker larvae were calculated by subtracting the average length of larvae at hatching (8.0 mm TL) from the total length at capture divided by 0.3 mm (Bestgen et al., 2002), which was the average daily growth rate of wild larvae observed by Muth et al. (1998) in the Green River UT. The back-calculated hatching formula was only applied to proto- and mesolarvae as growth rates become much more variable at later developmental stages (Bestgen, 2008). Spawning dates for Razorback Sucker are then calculated once hatching dates have been established using the negative exponential equation y = 1440.3e-0.109x (Bestgen et al., 2011) where y is the temperature dependent incubation time (in hours), e is the base of the natural logarithm, and x is the mean daily temperature on the hatching date. This study was initiated prior to spring runoff and completed in the middle of the summer season (early August). Daily mean discharge during the study period was acquired from U.S. Geological Survey Gages near Four Corners, CO (#09371010) and near Bluff, UT (#09379500). Temperature and discharge data analyzed included daily mean, minimum, and maximum values.

RESULTS

2017 Summary

The 2017 San Juan River larval fish survey took place between 16 April and 18 August 2017. Five trips were conducted from river mile 147.9 (Shiprock, NM) to river mile 2.9 (Clay Hills Crossing, UT), and three trips were conducted between river mile 180.6 (Animas River confluence in Farmington, NM) and river mile 147.9. During the first week of May, there was a high-volume and prolonged spring release out of Navajo Dam, which resulted in mean discharges over 5,000 cfs for 38 days and over 8,000 cfs for seven days during the study period (Figure 2). Mean daily discharge during the study period was 3,801 cfs (613–

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

8,540 cfs) and water temperature averaged 19.1oC (9.8–27.8oC). Our sampling collections (n = 289) encompassed 12,358.8 m2 of low-velocity habitat. The collections contained 30,227 age-0 and 1,348 age- 1+ fish representing six families and 16 species (Tables A-4 and A-5). Age-0 fish were collected in each of the eight surveys and accounted for 95.7% of the overall catch.

Colorado Pikeminnow (Age-0)

2017 Summary

There were 172 larval Colorado Pikeminnow collected in 2017 between river miles 162.5 and 8.1. Colorado Pikeminnow was collected between 23 and 27 July at 28 discrete localities with collections containing between one and 28 individuals (Figure 3). The larval seine collection at river mile 162.5 represents a 3.8-mile increase in upstream distribution for this species. This species was collected in Reach 6 in 2016 and 2017. The 2016 drift-net collection of this species was done as part of the evaluation of larval fish entrainment at the Hogback diversion canal. Two additional larval Colorado Pikeminnow were collected on 16 August downstream of the Piute Farms waterfall while we were assisting in the installation of a remote PIT tag antenna. Spawning by Colorado Pikeminnow in the San Juan River has been documented in ten of the last 15 years, and eight of the last nine. Colorado Pikeminnow (mesolarvae to recently transformed juveniles) ranged in size from 9.0 to 22.4 mm TL. Back-calculated spawning dates covered a 33-day period between 13 June and 16 July 2017 (Figure 4). Mean temperature and discharge during this period was 20.8oC (15.2–26.9oC) and 4,336 cfs (1,110–8,540 cfs), respectively.

Sampling-site density data

The analysis of Colorado Pikeminnow (age-0) sampling-site density data showed that (δ(Year) μ(Monitor) received 44.5% of the AICC weight (wi) and was the top model (Table 1). The fall Monitoring covariate for mu was found in the top six models for 2017, and collectively those models received nearly all (>99.9%) of the AICC weight. An analysis of deviance showed that this covariate accounted for 62.4% of the deviance explained by the μ(Year) (i.e. global) model over the μ(Null) (i.e. reduced) model (P < 0.01). Thus, the autumnal abundance of adult Colorado Pikeminnow explained most of the variation in larval fish densities recorded the following summer. In contrast, probabilities of occurrence values are poorly explained by both the abiotic and biotic covariates. Estimated densities (E(x)) of Colorado Pikeminnow in 2017, using sampling-site density data, were significantly higher (P < 0.05) than all preceding years except 2011, 2014, and 2016 (Figure 5). Estimated density could not be computed in 2009, as that year’s single non-zero value precluded mixture- model estimation of . Simple estimates of mean densities, using the method of moments, illustrated their close similarity with estimated densities over time. During 2016 and 2017, Colorado Pikeminnow was collected in reaches 6–1. This species was present in reaches 5 and 6 over the past two years. Densities were estimated using the long-term (2003– 2017) data set and were limited to reaches 5–1. The estimated density in Reach 5 was significantly lower (P < 0.05) than in reaches 4–1 (Figure 5).

Habitat type and location

Habitat data (2003–2017) were post-processed to generate five habitat categories (see Methods for definition of condensed habitat types). During the study period, larval Colorado Pikeminnow have been collected in backwaters, embayments, near zero velocity, and low velocity habitat types. Colorado Pikeminnow has not been collected in a run habitats (Figure 6). Within habitat types that contained Colorado Pikeminnow, estimated densities were significantly higher in backwaters (P < 0.05) than in near zero velocity and low velocity habitats (Figure 6). Within backwaters and embayments, there was no difference in estimated densities within the spatial location sampled (Figure 6).

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 2. Discharge (cfs) and temperature (oC) in the San Juan River during the 2017 sampling period. Grey vertical bars denote individual collecting trips between Shiprock NM and Clay Hills Crossing UT. Yellow vertical bars denote individual collecting trips between Farmington NM and Shiprock NM.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 3. Map of the 2017 age-0 Colorado Pikeminnow collection localities.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 4. Back-calculated spawning dates for Colorado Pikeminnow plotted against discharge and water temperature. USGS gage #09379500, Mexican Hat, UT.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 5. Colorado Pikeminnow (age-0) mixture-model estimates (E(x)), using sampling-site density data, by year (top graph) and reach (bottom graph). Solid circles indicate estimates, and bars represent 95% confidence intervals. Red diamonds indicate simple estimates of mean densities using the method of moments.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

2017 trip and reach

Larval Colorado Pikeminnow was collected in reaches 6–1 between river miles 162.5 and 8.1 (Figures 3). For the third consecutive year, larval Colorado Pikeminnow was only collected in the middle and lower sections during the late July survey. The single collection of Colorado Pikeminnow in the upper section was also taken in late July. All three sections within the study area were sampled during the same week (23–27 July). Prior to 2015, nearly 99.0% of all Colorado Pikeminnow were collected during the mid-July survey. During the late July survey, larval Colorado Pikeminnow was found in 28 of the 67 collections. Densities increased between Reaches 6–3 and decreased between Reaches 3–1 (Figures 7 and B-1).

Colorado Pikeminnow (age-1+)

Sampling-site density data

During 2017, age-1+ Colorado Pikeminnow was found in every habitat type sampled except runs. Four of the five survey trips within the middle and lower sections, and one of the survey trips within the upper section (late July) produced age-1+ Colorado Pikeminnow. A total of 233 individuals (size range 28–250 mm SL) were collected in 2017. Over half (n = 138) were found in the middle and lower sections during the April survey. This monthly total was greater than most annual totals since the beginning of this study. The estimated densities of age-1+ Colorado Pikeminnow in 2017, using sampling-site density data, were significantly higher (P < 0.05) than 2003, 2004, 2006, 2011, 2013, and 2015 (Figure 8). Estimated densities fluctuated between a low of 0.2 fish per 100 m2 in 2011 and a high 2.2 fish per 100 m2 in 2017. The majority of age-1+ Colorado Pikeminnow collected since 2003 appear to be the result of augmentation efforts. A strong reproductive year in 2016, which was documented by both the larval and small-bodied monitoring programs, suggests some number of Age-1 fish collected in 2017 were wild individuals. Nearly 5.5 million age-0 and age-1 Colorado Pikeminnow have been stocked into the San Juan River since 2003.

Razorback Sucker (age-0)

2017 Summary

Age-0 Razorback Sucker were collected during each of the five surveys within the middle and lower sections and one of three surveys in the upper sections. Ontogenetic stages of the 360 age-0 Razorback Sucker ranged from protolarvae to juvenile (size range = 9.2–43.0 mm TL). Razorback Sucker larvae were collected in reaches 6–1 and distributed between river miles 155.9 and 5.6 (Figure 9). Similar to Colorado Pikeminnow, larval Razorback Sucker was collected as part of the evaluation of larval fish entrainment at the Hogback diversion canal in 2016. For the second consecutive year, Razorback Sucker larvae were collected in Reach 6. Their upstream distribution was similar in 2016 and 2017 (river mile 158.7 and 155.9, respectively). Spawning by Razorback Sucker in the San Juan River has been documented for 20 consecutive years. Back-calculated spawning dates for the larval fish survey extended from 23 March to 9 July 2017 (Figure 10). Mean temperature and discharge during this period was 15.2oC (9.8–26.5 oC) and 4,250 cfs (1,130–8,540 cfs).

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Table 1. General linear models of Colorado Pikeminnow (age-0) mixture-model estimates (delta (δ)1and mu ()2), using sampling-site density data (2003–2017) and covariates, allowing for random effects (R). Models are ranked by Akaike’s information criterion (AICC) and include the AICC weight (wi).

3 4 5 Model K logLike AICC wi

δ(Year) (Monitor) 19 750.36 788.79 0.457

δ(Year) (July temp+Monitor) 21 747.13 789.67 0.295

δ(Year) (June temp+Monitor) 21 749.34 791.87 0.098

δ(Year) (June flow+Monitor) 21 749.69 792.22 0.082

δ(Year) (July flow+Monitor) 21 750.34 792.87 0.059

δ(Year) (Monitor+R) 20 756.53 797.02 0.007

δ(Year) (July temp+Cum.Stocked) 21 763.30 805.84 <0.001

δ(Year) ( Cum.Stocked+R) 20 766.32 806.80 <0.001

δ(Year) (Cum.Stocked) 19 770.25 808.69 <0.001

δ(Year (June temp+R) 20 770.45 810.93 <0.001

1 = probability of occurrence 2 = mean of the lognormal distribution 3 = Model variables included year, reach, mean June flow and temperature, mean July flow and temperature, cumulative number stocked, and fall monitoring captures (400+mm TL). 4 = Number of parameters in the model 5 = -2[log-likelihood] of the model

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 6. Colorado Pikeminnow (age-0) mixture-model estimates (E(x)), using sampling-site density data (2013–2017) and habitat covariates, by habitat type (top graph) and spatial location (bottom graph). Solid circles indicate estimates and bars represent 95% confidence intervals. Red diamonds indicate simple estimates of mean densities using the method of moments.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 7. Density (fish per 100 m2 of area sampled) of age-0 and age-1 Colorado Pikeminnow (Ptyluc and Ptyluc1, respectively) and age-0 Razorback Sucker (Xyrtex) by trip (top graph) and reach (bottom graph) during the 2017 survey.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 8. Colorado Pikeminnow (age-1+) mixture-model estimates (E(x)) using sampling-site density data (2003–2017). Solid circles indicate estimates and bars represent 95% confidence intervals. Red diamonds indicate simple estimates of mean densities using the method of moments.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Sampling-site density data

General linear models of Razorback Sucker mixture-model estimates revealed that the (δ(year) μ(May flow + cumulative# stocked)) model received 78.3% of the AICC weight (wi) (Table 2). The May flow covariate for mu was present in four of the five top models. Together, these four models received nearly 98.2% of the AICC weight. The covariate (May flow + cumulative# stocked) accounted for 43.2% of the deviance explained by the μ(Year) over the null μ(.) model (P < 0.001). Estimates of mu (μ) decreased as May discharge increased. This suggests drifting larval Razorback Sucker are being displaced below the Paiute Farms waterfall, negatively impacted by cooler river temperatures associated with higher May discharge, or a combination of both. Between 1999 and 2017, Razorback Sucker estimated densities, using sampling-site density data, were highest in 2015 (27.4 fish per 100 m2) and lowest in 1999 (0.2 fish per 100 m2). The estimated densities of Razorback Sucker in 2017 were significantly lower (P < 0.05) as compared to 2002 and 2011–2016 and significantly higher than 1999, 2004, and 2005 (Figure 11). Among reaches, estimated densities were highest in Reach 1 (P < 0.05), between 1999 and 2017, with no significant differences between reaches 5–2 (Figure 11). While there were no significant differences across reaches 5–2 from 2014 to 2017, annual estimated densities varied considerably in Reach 4. Estimated densities have risen from 3.6 fish per 100 m2 in 2014 to 5.2 fish per 100 m2 in 2017. This suggests Razorback Sucker adults are becoming more abundant and established in the San Juan River within and upstream of Reach 4. Both the larval fish monitoring, and the adult monitoring programs support this assertion (Schleicher, 2017).

Habitat type and location

Within the habitats sampled between 1999 and 2017, estimated densities were significantly higher in backwaters (P < 0.05) when compared to run, embayment, and low velocity habitat types (Figure 12). Estimated densities were also significantly lower (P < 0.05) in run habitats compared to all other habitat types. Within backwaters and embayments, there were no significant differences in densities across spatial locations (Figure 12). This was different than previous survey years when densities at the terminal end were significantly higher than densities within the mouth of backwaters and embayments. Similar to previous survey years, the sampling order was kept random so that the mouth was not always the first location sampled, and the terminus was not always the last. It is recognized that these results can potentially be influenced by the sampling activities of the researchers, (i.e., “herding” larvae to the terminal end by sampling from the mouth to the terminus).

2017 Trip and Reach

Within the middle and lower study areas, larval Razorback Sucker was collected during each of the five larval fish surveys (Figure 7). Within the upper section, a single larval Razorback Sucker was collected in the late July survey just downstream of the Hogback diversion canal. For the sixth time since this study began, larval Razorback Sucker was collected during the April survey. The 2017 larval fish survey marks four consecutive years of captures during the April trip. Densities were highest during May, when 69.7% (n = 251) of the 2017 total were collected. The single largest collection of Razorback Sucker larvae also occurred in May, with 156 fish collected from the Steer Gulch monitoring site at river mile 8.1. Five juvenile Razorback Sucker, including the largest individual encountered in 2017 (a 43.0 mm TL juvenile), were collected during the June survey in a backwater located at river mile 79.3 (Cottonwood Draw). Densities of larval Razorback Sucker were highest in Reach 1 (8.9) and lowest in Reach 6 (0.07 [Figures 7 and B-1]). This pattern of increasing larval Razorback Sucker densities from upstream to downstream has been observed throughout the tenure of this study.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 9. Map of the 2017 age-0 Razorback Sucker collection localities.

Figure 10. Back-calculated spawning dates for Razorback Sucker plotted against discharge and water temperature. USGS gage #09379500, Mexican Hat, UT.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Table 2. General linear models of Razorback Sucker (age-0) mixture-model estimates (delta (δ)1 and mu ()2), using sampling-site density data (1999–2017) and covariates allowing for random effects (R). Models are ranked by Akaike’s information criterion (AICC) and include the AICC weight (wi).

3 4 5 Model K logLike AICC wi

δ(Year) (May flow+Cum.Stocked) 25 4,030.69 4,081.11 0.783

δ(Year) (May flow+Monitor) 25 4,033.78 4,084.19 0.167

δ(Year) (May flow+ R) 24 4,039.92 4,088.30 0.021

δ(Year) (Year) 22 3,973.19 4,089.31 0.013

δ(Year) (May flow) 23 4,043.24 4,089.59 0.011

δ(Year) ( May temp+Cum.Stocked) 25 4,041.24 4,091.66 0.004

δ(Year) (April flow+Cum.Stocked) 25 4,045.71 4,096.12 <0.001

δ(Year) (April flow+R) 24 4,050.57 4,098.95 <0.001

δ(Year) (April temp+Cum.Stocked) 25 4,050.31 4,100.72 <0.001

δ(Year) (Cum.Stocked+R) 24 4,052.90 4,101.28 <0.001

1 = probability of occurrence 2 = mean of the lognormal distribution 3 = Model variables included year, reach, mean March flow and temperature, mean April flow and temperature, mean May flow and temperature, annual number stocked, cumulative number stocked (Cum.Stock), and fall monitoring captures (Monitor) 4 = Number of parameters in the model 5 = -2[log-likelihood] of the model

22 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 11. Razorback Sucker (age-0) mixture-model estimates (E(x)) using sampling-site density data by year (top graph) and reach (bottom graph). Solid circles indicate estimates and bars represent 95% confidence intervals. Red diamonds indicate simple estimates of mean densities using the method of moments.

23 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 12. Razorback Sucker (age-0) mixture-model estimates (E(x)), using sampling-site density data (2013–2017) and habitat covariates, for habitat type (top graph) and location within backwaters and embayments (bottom graph). Solid circles indicate estimates and bars represent 95% confidence intervals.

24 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Common Species Data from the Middle and Lower Sections (Long-term dataset)

Bluehead Sucker. Estimated densities (E(x)) of Bluehead Sucker were highest in 2013 (111.8) and lowest in 2009 (7.8). Estimated densities in 2017 were significantly lower (P < 0.05) than 2004, 2005, 2007 and 2012–2014 (Figure 13). The 2,026 age-0 specimens collected accounted for 20.2% of the 2017 catch, and Bluehead Sucker was found in 36.8% of all collections. Larval Bluehead Sucker was first collected during the May survey with the highest densities occurring during the late-July survey (Figure 14). Within reaches, densities were highest in Reach 5 and lowest in Reach 1 (Figure 14). The temporal and spatial density patterns of Bluehead Sucker in 2017 were nearly identical to that of 2016.

Flannelmouth Sucker. Larval Flannelmouth Sucker was first collected during the April survey, and densities peaked the following month (Figure 14). Densities were highest in Reach 3 (Figure 14) and appeared to be influenced by McElmo Creek at river mile 100.5. Nearly 60% of all larval Flannelmouth Sucker collected in Reach 3 were found within McElmo Creek, or less than four miles downstream of the confluence with the San Juan River. Larval Flannelmouth Sucker collected in 2017 (n = 4,301) accounted for 42.9% of all fish larvae. During 2017, flannelmouth Sucker was found in 42.9% of collections, and had the highest frequency of occurrence of any species. Estimated densities (E(x)) were highest in 2008 (358.7 fish per 100 m2) and lowest in 2013 [18.8 fish per 100 m2 (Figure 15)]. Estimated densities in 2017 were significantly lower (P < 0.05) than 2007, 2008, 2011, 2012, and 2015 (Figure 15).

Speckled Dace. In 2017, Speckled Dace estimated densities were significantly higher (P < 0.05) than 2003 and not significantly different than other years (Figure 16). Estimated densities (E(x)) of larval Speckled Dace were highest in 2004 (132.8) and lowest in 2003 (9.7). Larval Speckled Dace were first collected during the May survey, and densities were highest during the late July survey (Figure 17). Densities of larval Speckled Dace were highest in Reach 5 and lowest in Reach 1. The temporal and spatial density patterns of Speckled Dace in 2017 were similar to those of 2016 (Figure 17). Speckled Dace was found in 31.8% of all samples and made up 22.7% of the total catch.

Red Shiner. Similar to 2015 and 2016, estimated densities in 2017 (E(x) = 6.0) were among the lowest of any year during the study period and were several orders of magnitude lower than the highest (3,725.1) estimated density of 2005 (Figure 18). Red Shiner estimated densities in 2017 were significantly lower (P < 0.05) than any previous year except 2015 and 2016 (Figure 18). Red Shiner larvae were first collected during the June survey, with the highest densities occurring during the late July survey (Figure 17). Among reaches, densities were highest in Reaches 4 and 3 and nearly identical in Reaches 5, 2 and 1. The 234 Red Shiner larvae collected accounted for 2.3% of the total catch and were found in 14.4% of the collections.

Fathead Minnow. Fewer larval Fathead Minnow were collected in 2017 (n = 57) than in any other sampling year. This contrasts with 2016 when larval Fathead Minnow were the numerically dominant (n = 762) nonnative species. In 2017, estimated densities were significantly lower (P < 0.05) than in all preceding years except 2009 and 2015 (Figure 19). Estimated densities (E(x)) were highest in 2003 (168.8) and lowest in 2009 (0.7). Larval Fathead Minnow were first encountered during the May survey, absent from the two subsequent surveys, and most abundant during the late July survey (Figure 17). Densities were highest in Reach 5 and similar in Reaches 4–2, but none were found in Reach 1 (Figure 17). Larval Fathead Minnow made up 0.6% of the 2017 catch, and it was found in 5.4% of all collections.

25 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 14. Density (fish per 100 m2 of area sampled) of age-0 Bluehead Sucker (Catdis) and Flannelmouth Sucker (Catlat) by trip (top graph) and reach (bottom graph) during the 2017 survey.

27 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 15. Flannelmouth Sucker (age-0) mixture-model estimates (E(x)) using sampling-site density data (2003–2017). Solid circles indicate estimates and bars represent 95% confidence intervals. Red diamonds indicate simple estimates of mean densities using the method of moments.

28 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 17. Density (fish per 100 m2 of area sampled) of age-0 small-bodied cyprinids: Red Shiner (Cyplut), Fathead Minnow (Pimpro), and Speckled Dace (Rhiosc) by trip (top graph) and reach (bottom graph) during the 2017 survey.

30 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Common Carp. Estimated densities (E(x)) for age-0 Common Carp were highest in 2004 (2.3) and lowest in 2017 (0.1 [Figure 20]). Estimated density could not be computed in 2003 and 2006, as single non-zero values in those years precluded mixture-model estimation of . Estimated densities in 2017 were not significantly higher than any previous year but were lower (P < 0.05) than 2004, 2005, 2007–2009, and 2011 (Figure 20). Overall, estimated densities remained the lowest of any species for which mixture-model estimations were derived. Larval Common Carp were collected during a three-week period encompassing the mid- and late July surveys (Figure 21). Common Carp were only present in reaches 5 and 1, with densities highest in Reach 5 (Figure 21). The seven individuals collected in 2017 were found in 5 discrete collections and made up less than 0.01% of the total catch

Channel Catfish. Larval Channel Catfish were collected during one survey (late July) during 2017 (Figure 21). Despite not being present in Reach 5, age-0 Channel Catfish were found in nearly half of the collections during the late July survey. Similar to most survey years, Channel Catfish densities were highest in Reach 2 (Figure 21). Estimated densities (E(x)) were highest in 2007 (36.9) and lowest in 2015 (1.0 [Figure 23]). Estimated densities in 2017 were significantly lower (P < 0.05) than 2007, 2008 and 2014 (Figure 22).

2017 Razorback Sucker opercular deformities.

In 2017, age-0 Razorback Suckers were rated for opercular deformities using the methods outlined in a previous investigation (1998–2012) of native suckers (Barkstedt et al., 2014). The opercular deformity study completed in 2013 rated all three native suckers in collections from 1998 to 2012 (n = 55,385). Between 1998 and 2012, opercular deformities were found in 4.3% of Bluehead Sucker (n = 8,565), 6.3% of Flannelmouth Sucker (n = 45,416), and 23.6% of Razorback Sucker (n = 1,404). In 2017, Razorback Sucker individuals (>15 mm TL) were rated bilaterally for deformed opercula (0 = none, 1 = slight shortening, and 2 = severe shortening). We examined 145 specimens and found that 18 exhibited deformed opercula (Figure 23). Of the 145 fish rated, most were either meso- or metalarvae; only 17 were recently transformed juveniles. While fish were rated for deformities in reaches 4–1 (none collected in Reach 5), deformed fish were only found in reaches 3–1. Deformities were found bilaterally (3.4%, n = 5) and unilaterally (9.0%, n = 13). A severe deformity (a rating of 2) was only found in a single fish. The deformity rate in 2017 (13.1%) was slightly lower than that documented in 2016 (17.6%).

Monitoring sites

During 2017, the 15 monitoring sites were visited 75 times (Table A-3). Each site was sampled if suitable nursery habitat was available, otherwise photographs were taken and conditions noted on a field data sheet. During our 75 visits, backwater habitats were encountered 55 times, isolated pools were found 6 times, and sites were dry 13 times. On one occasion during the late July survey, water was flowing into the monitoring site at river mile 92.2 (Montezuma Creek) from the surrounding landscape. During this visit, run habitat was encountered and not sampled. The highest level of connectivity (100%) observed during 2017 was during the April and June surveys, with the lowest (13.3%) occurring during the mid-July survey (Figure 24). Overall, monitoring sites were connected to the river 74.7% of the time during 2017. Two monitoring sites located at river mile 17.7 (Slickhorn Canyon) and 8.1 (Steer Gulch) were connected to the river during every survey trip. During 2017, collections encompassing 3,131.7 m2 of habitat were made at monitoring sites. These collections contained 3,334 age-0 fish, including 288 larval Razorback Sucker. This represents 80.2% of the 2017 larval Razorback Sucker total, which were collected in 30.3% of the total habitat sampled. We also collected 11 larval and 84 Age-1+ Colorado Pikeminnow from the monitoring sites.

31 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

32 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

33 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

34 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 21. Density (fish per 100 m2 of area sampled) of age-0 Common Carp (Cypcar) and Channel Catfish (Ictpun) by trip (top graph) and reach (bottom graph) during the 2017 survey.

35 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

36 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 23. Percentage of Razorback Sucker with opercular deformities by year. The number of fish examined is reported in parentheses.

37 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Figure 24. Mean connectivity of the 15 monitoring sites during the five survey trips denoted by gray bars.

38 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Phase I RERI sites

During the 30 RERI site visits, seven collections yielded nine species and a total of 168 age-0 and 40 age-1+ fish (Table 3). In 2017, for the first time since the completion of these restored habitats, neither age-0 Colorado Pikeminnow nor Razorback Sucker was collected. The magnitude and duration of the spring release from Navajo reservoir meant that run habitats were often encountered at the phase I restoration sites. Collections were usually not made when run habitats were encountered. In 2017, we collected age-1 Colorado Pikeminnow (n = 14) within RERI sites. An effort was made to compare the six RERI sites to other, similar sites sampled in 2017. Capture data were separated for all sites located within the same five river miles as the RERI sites, and for all sites within five miles up or downstream of the RERI sites (RM 137.2–122.2). Within this pool of sites, all habitats associated with washes, arroyos, or tributaries were excluded from analysis. The remaining sites (n = 10) were all habitats that were directly associated with either main or secondary channels. Similar to the seven collections made within the RERI sites, not all of these sites contained fish during sampling. These ten sites were considered the “control” sites. Control sites contained 989 native and 21 nonnative age-0 fish, including two Colorado Pikeminnow larvae. The higher number of age-0 fish collected, and the higher proportion of native species collected was primarily the result of a backwater habitat sampled at river mile 132.8 during the late July survey. This collection contained 641 native age-0 fish, including the aforementioned larval Colorado Pikeminnow. Backwaters were not encountered during any of the survey trips at the Phase I restoration sites during 2017.

Upper section (Farmington reach) summary

Three larval fish surveys, from 6 June to 18 August, were conducted in the San Juan River between Farmington and Shiprock, NM. The June survey was done during peak runoff and produced very few (n = 70) age-0 fish. The late July and mid-August surveys were conducted after runoff and produced over 20,000 age-0 fish, including three larval Colorado Pikeminnow and one Razorback Sucker (Table 4). This section of the river was dominated by native species, particularly Bluehead Sucker and Speckled Dace. Densities for both of these species in 2017 were highest upstream of Shiprock (Figure B-1). The number of Bluehead Sucker (n = 10,598) was greater than the total number of age-0 fish collected during the five surveys conducted downstream of Shiprock. Densities of Flannelmouth Sucker were lower than in Reach 3 downstream, but similar to other downstream reaches. This was in spite of the fact that sampling in this upper reach occurred later (June–August) than the typical peak occurrence (May–June) of larval Flannelmouth Sucker. Nonnative species collected in the upper section included White Sucker and Bluegill, which were not found downstream of Shiprock. Overall numbers and densities of Common Carp, Fathead Minnow, Plains Killifish, Western Mosquitofish, and Largemouth Bass were all higher between Farmington and Shiprock (Table 4, Figure B-1). Red Shiner densities were lower than in Reach 4 downstream, but similar to other downstream reaches. Notably absent from this reach was any species of catfish (Figures B-1). Combined, the 20,209 age-0 fish collected from this reach constituted 66.8% of the 2017 age-0 total.

39 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Table 3. Species composition and habitat type of the six RERI sites sampled in 2017. Six letter species codes are defined in Table A-6.

RERI (RM) Survey Month Water Descriptor CFS @ FC PTYLUC 0 PTYLUC 1 RHIOSC CATDIS CATLAT XYRTEX NON-NATIVE Sp. 132.2 April Embayment 3,000 5 May Slackwater 4,980 June Run 8,310 Mid-July Site Dry 914 Late July Site Dry 954 Total 5

132 April Run, not sampled 3,000 May Run, not sampled 5,120 June Run, not sampled 8,310 Mid-July Run/sand shoal not sampled 914 Late July Run/sand shoal not sampled 954 Total

130.7 A April Run, not sampled 3,000 May Run, not sampled 5,120 June Run, not sampled 8,310 Mid-July Slackwater 914 9 2 3 Late July Slackwater 954 3 2 Total 12 2 5

130.7 B April Run, not sampled 3,000 May Run, not sampled 5,120 June Run, not sampled 8,310 Mid-July Run, not sampled 914 Late July Run, not sampled 954 Total

128.6 April Run 3,000 May Run, not sampled 5,120 June Run, not sampled 8,310 Mid-July Pool 914 2 3 2 42 Late July Pool 954 32 44 1 2 Total 34 47 3 44

127.2 April Slackwater 3,000 9 May Run, not sampled 5,120 June Run, not sampled 8,310 Mid-July Slackwater 914 5 4 5 Late July Pool 954 2 4 Total 9 7 4 9

40 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Table 4. Species composition of Age-0 and Age-1+ fish collected between river mile 180.6 and 147.9 (Farmington to Shiprock, NM).

Species (common name) Age-0 (n = ) Age-1+ (n = )

Common Carp 75 2 Colorado Pikeminnow 3 4 Fathead Minnow 819 95 Red Shiner 29 4 Speckled Dace 7,864 21 Bluehead Sucker 10,598 1 Flannelmouth Sucker 450 3 Razorback Sucker 1 0 White Sucker 12 0 Black Bullhead 0 0 Channel Catfish 0 0 Plains Killifish 13 0 Western Mosquitofish 318 172 Bluegill 2 0 Green Sunfish 2 1 Largemouth Bass 23 1 TOTAL 20,209 304

41 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

DISCUSSION

For the second consecutive year, a prolonged spring release of water from Navajo Reservoir was made into the San Juan River. The number of days with high flows (> 5,000 cfs and > 8,000 cfs) was among the highest recorded during the tenure of this study. Conversely, the number of days with base flows (500–1,000 cfs) was among the lowest. Prolonged periods of higher discharge, coupled with minimal days at base flows, have been shown to mobilize and re-deposit cobble bars (i.e. creation of spawning habitat), increase total wetted area, and increase the number and size of backwater habitats [i.e., the creation and maintenance of nursery habitat (Lamarra and Lamarra, 2017)]. One negative consequence of prolonged periods of elevated discharge, from hypolimnetic dam releases, is the suppression of river temperatures (Miller, 2016). Cold water has been shown to delay spawning in adult fish, decrease larval fish growth rates, decrease food consumption and assimilation efficiency, lower survival rates, and increase larval drift time (Lagler et al. 1977, Hamman 1982, Marsh 1985, and Bestgen, 2008). Based on a study of passively drifting particles at moderate (1,000–3,600 cfs) flows, Dudley and Platania (2000) found that Colorado Pikeminnow could be transported the entire length of the critical habitat (approximately 340 kilometers) in as little as four days. Cold water, coupled with the relatively high gradient of the San Juan River, likely results in larval fishes drifting over the Paiute Farms waterfall and being lost to Lake Powell. The results of the 2017 larval fish survey indicate that a notable portion of larvae are likely being displaced downstream and into Lake Powell during high discharge events. The 10,030 larval fish collected between Shiprock, NM and Clay Hills Crossing, UT (the long-term study area) was the lowest number recorded during the tenure of this study. The second lowest total recorded was the 12,973 larvae collected in 2016, which was another high discharge year. While an additional 20,209 larvae were collected in 2017 from the study area upstream of Shiprock, over 99% of these fish (n = 20,139) were collected during survey trips that occurred after spring runoff. Over half of all larvae collected in the upper section were Bluehead Sucker. The core of the adult Bluehead Sucker population resides upstream of Reach 5 with no significant changes in adult abundance observed over the last 17 years (Schleicher, 2017). Mixture model analyses provide further evidence of the potential effects of elevated spring flows on larval Razorback Sucker densities. The May flow covariate for mu (μ) was present in four of the five top models, and these four models received nearly 98.2% of the AICC weight. These ecological models show that larval densities tend to decrease as a function of increasing discharge during May. While the importance of high flow events in the creation and maintenance of spawning habitat, channel complexity, and nursery habitats cannot be overstated, the trade off may be the loss or reduction of an annual cohort of larval fishes within the river due to displacement below the waterfall. This is not meant to imply that larval drift was not evolutionally advantageous, or that larvae below the waterfall are incapable of survival. What is certain is that larvae that are displaced below the waterfall are cutoff from the river upstream. The larval fish surveys continue to document the importance of backwater habitats, which typically occur in lateral canyons and washes (i.e., commonly found at our monitoring sites). These habitats are particularly important for Razorback Sucker whose recruitment period from larvae to early juveniles coincides with elevated spring discharge. The vast majority of larval Razorback Sucker came from lateral washes and canyons in 2016 and 2017 (81.9% and 97.2%, respectively). Throughout the tenure of this study, the densities of Razorback Sucker larvae are often highest at the monitoring sites. The connectivity of monitoring sites was unusually high in 2017, and these habitats proved important for Colorado Pikeminnow. We collected 11 larval and 84 Age-1+ Colorado Pikeminnow from these areas in 2017. The productivity of backwaters associated with monitoring sites may be caused by their increased likelihood for persisting, as compared with other backwaters found in the San Juan River. In their Detailed Reach Study, Bliesner et al. (2009) reported that less than 4% of backwaters present in May had persisted until June. This contrasts sharply with the overall connectivity rate of 75% for monitoring sites in 2017, with two locations connected to the San Juan River over the entire study period. When connections to the main stem are lost because of declining flows, large isolated pools can form in these lateral canyons and washes. These areas can provide temporary refuge for larval fishes if rising flows (e.g., monsoonal rains) can flush sand bar plugs and re-establish habitat/river connectivity. This flushing

42 American Southwest Ichthyological Researchers, L.L.C. Funding: U.S. Bureau of Reclamation Contract GS-10F-0249X

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018 of sediment from the mouth of monitoring sites by rain events is well documented by this study. Unlike backwaters at the downstream end of secondary channels that may not see sufficient flows to remove sediment and encroaching vegetation for several years, lateral canyons and washes are nearly always flushed and maintained by annual monsoonal rain events. While the sampling methodology used in the newly expanded study area between Farmington and Shiprock, NM was consistent with the long-term larval fish monitoring, the goals of these efforts were unique. The primary objective in 2017 was to document the upstream distribution of larval Colorado Pikeminnow and Razorback Sucker. We used a flexible yet intensive sampling approach to help ensure that adequate numbers of larval fish were collected to document the presence of rare species in the upper section. While the timing of surveys for the long-term study area has been kept consistent for the past 15 years, survey dates for the upper study area were based on presence and abundance of larval fish documented during survey trips within the long-term study area. While this “adaptive sampling” methodology could initially result in substantial variation in the year-to-year timing of surveys, the success of this technique was evidenced by the collection of both endangered species and a large number of age-0 fish (> 20,000 in 2017). Should sampling of the upper section continue for several years, it is anticipated that the sampling dates would become more standardized. Similar to the middle and lower sections, optimal sampling periods can be elucidated through time.

Management implications.

The data generated from larval fish monitoring is both timely and relevant to several management actions currently being considered by the SJRBRIP. During years when there is insufficient water available to make a spring reservoir release, but enough to meet end-of-water-year storage targets, it may still be possible to increase summer base flows to create nursery habitats. Our long-term monitoring efforts, coupled with insights from other SJRBRIP studies, have shown the importance of nursery habitats (e.g., backwaters in lateral canyons and washes) to the growth and survival of larval native fishes in the San Juan River. In coordination with the current habitat monitoring program, it may be possible to target an optimal elevated discharge that increases the total area of backwater habitats, inundates a majority of lateral canyons and washes, and does so while using the least amount of water possible. By maximizing the use of available water, the SJRBRIP would also be able to prolong the persistence of crucial nursery habitats. The larval fish monitoring could then be used to evaluate and help optimize the success of different management actions. The larval monitoring program has also been instrumental in documenting the success of recent habitat restoration projects (e.g., RERI). Currently, the SJRBRIP is considering whether or not to proceed with an RERI phase III restoration project. A wetland habitat, similar to those successfully implemented for Razorback Sucker in the Green River (Bestgen, 2011), would be constructed for this proposed project. While a constructed wetland would be fundamentally different from currently available habitats in the San Juan River, it shares similar characteristics with some of the long-term monitoring sites. As noted earlier, the persistence of large backwaters at these monitoring sites is likely promoting the growth and survival of age-0 Razorback Sucker. The Phase III RERI site would provide larval fish with similarly stable habitats during the crucial summer growing season. One management option being considered for the Phase III wetland site is to “seed” it with San Juan River larvae if sufficient numbers aren’t entrained into it naturally. The larval monitoring program could help identify sites and habitats with high densities of native fish larvae (particularly Razorback Sucker) for stocking into the wetland. Finally, the results of fish reared within the wetland (i.e., species composition, number, and size) could be compared to the larval fish survey results to help determine the relative success of the constructed wetland. Data from the long-term monitoring effort can be used by the SJRBRIP to determine when to implement Reasonable and Prudent Measures (RPM) necessary to avoid adverse impacts to the endangered fish species. Sampling in the upper section to document the upstream distribution of both endangered fish species may trigger RPM #2, as outlined in the Biological Opinion for Four Corners Power Plant (Service, 2015). If either larval Colorado Pikeminnow or Razorback Sucker larvae were collected upstream of river mile 163.7 (APS pumping station), a feasible pumping plan that maintains the current operating configuration could be developed to help minimize entrainment risk. The long-term nature of this study has revealed key ecological and habitat relationships, tracked

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018 backwater persistence, and documented range expansion by both endangered species. These data have been used to guide programmatic decisions regarding flow recommendations, construction of restored habitats, and identification of recruitment bottlenecks for both species. Larval fish monitoring will continue to provide the SJRBRIP with data necessary to evaluate endangered species progress towards recovery, determine the success of restored habitats, and inform management decisions that will assist in the recovery of Colorado Pikeminnow and Razorback Sucker in the San Juan River.

ACKNOWLEDGMENTS

Numerous individuals assisted with the efforts necessary to accomplish this project. Adam L. Barkalow, Bruce L. Christman, Meredith C. Campbell, Martinique J. Chavez, Scott L. Durst (USFWS), Austin L. Fitzgerald, Curtis A. Peralta and Aaron C. Wedemeyer assisted in the field portion of the study. Brandt G. Hart, Linda M. Richmond and Silas Sparks (BLM) helped coordinate departure dates and camping logistics. Assistance with all aspects of collection, database management, and curation was provided by Alexandra M. Snyder (UNM, MSB). Collections were prepared for identification and curation by Yvonne Rivera, Carly Cleghorn, and Alondra Toca Diaz (UNM, MSB). Data necessary for the completion of this report was freely shared by Scott L. Durst, D. Weston Furr, and Benjamin J. Schleicher (all USFWS). Scott L. Durst, Dr. Thomas A. Wesche, and Matthew P. Ziegler reviewed and commented on earlier drafts. This study was approved by the San Juan River Basin Biology Committee through the San Juan River Basin Recovery Implementation Program and funded under a U. S. Bureau of Reclamation, Salt Lake City Project Office Award #GS-10F-0249X administered by Dr. Mark C. McKinstry and Melanie S. Russell (U.S. Bureau of Reclamation). The collecting of fish was authorized under scientific collecting permits provided by the Navajo Nation, New Mexico Department of Game and Fish, U.S. Fish and Wildlife Service and Utah Division of Wildlife Resources.

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APPENDIX A

Figure A-1. Example of field data recorded at each sampling locality.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Table A-1. Summary of larval Colorado Pikeminnow in the San Juan River (1993–2017) and back-calculated dates of spawning.

Number of Distribution Year Specimens Spawning dates (river miles) Sample Method

1993 2 8–9 July 53.0 drift netting

1995 2 15–17 July 53.0 drift netting

1996 1 18 July 127.5 drift netting

2001 1 17 July 127.5 drift netting

2004 2 24–25 June 17.0 – 46.3 larval seine

2007 3 27 June 33.7 – 107.7 larval seine

2009 1 10 June 24.7 larval seine

2010 5 15–27 June 13.0 – 58.9 larval seine

2011 29 23 June –12 July 7.0 – 92.6 larval seine

2013 12 23 May – 3 July 10.0 – 107.6 larval seine

2014 312 15 June – 2 July 3.2 – 116.9 larval seine

2015 24 10 July – 14 July 57.2 – 94.8 larval seine

2016 548 29 June – 12 July 147.1 – 5.0 larval seine

2017 174 13 June – 16 July 155.9 – (-1.0) larval seine

Total 1,116

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Table A-2. Summary of larval and age-0 Razorback Sucker collected during the San Juan River larval fish survey 1998–2017.

Year Study Area Project Dates Total Effort m2 Xyrtex Sample Method

1998 127.5 - 53.0 17 Apr – 6 Jun - 2 larval seine/ light trap

1999 127.5 - 2.9 5 Apr – 10 Jun 2,713.5 7 larval seine/ light trap

2000 127.5 - 2.9 4 Apr – 23 Jun 2,924.6 129 larval seine/ light trap

2001 141.5 - 2.9 10 Apr – 14 Jun 5,733.1 50 larval seine/ light trap

2002 141.5 - 2.9 15 Apr – 12 Sep 9,647.5 815 larval seine/ light trap

2003 141.5 - 2.9 15 Apr – 19 Sep 13,564.6 472 larval seine

2004 141.5 - 2.9 19 Apr – 14 Sep 11,820.3 41 larval seine

2005 141.5 - 2.9 19 Apr – 14 Sep 10,368.6 19 larval seine

2006 141.5 - 2.9 17 Apr – 15 Sep 12,582.6 202 larval seine

2007 141.5 - 2.9 16 Apr – 19 Sep 13,436.0 200 larval seine

2008 141.5 - 2.9 14 Apr – 13 Sep 14,292.3 126 larval seine

2009 141.5 - 2.9 13 Apr – 26 Sep 15,860.3 272 larval seine

2010 141.5 - 2.9 19 Apr – 3 Sep 16,761.0 1,251 larval seine

2011 141.5 - 2.9 13 Apr – 26 Sep 9,387.9 1,065 larval seine

2012 147.9 - 2.9 16 Apr – 9 Aug 8,269.8 1,778 larval seine

2013 147.9 - 2.9 21 Apr – 2 Aug 9,750.0 979 larval seine

2014 147.9 - 2.9 21 Apr – 31 July 8,623.0 612 larval seine

2015 147.9 - 2.9 19 Apr – 30 July 8,886.4 1,205* larval seine

2016 147.9 - 2.9 17 Apr – 28 July 10,493.6 824 larval seine

2017 180.6 - 2.9 16 Apr – 18 August 12,358.8 360 larval seine

TOTAL 10,409

* The 2015 total includes larval fish recaptured from a stocking at the Hogback Diversion (RM 158.8)

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Table A-3. Locality and description of the 15 monitoring sites designated for habitat persistence.

River Mile Reach Easting Northing Locality description

124.8 4 678281 4091267 lateral wash river left

119.5 4 675632 4096476 lateral wash river left

118.5 4 674456 4097745 lateral wash river left

116.9 4 673442 4100108 lateral wash Cowboy Wash

104.4 3 663008 4115111 lateral wash river left

96.4 3 654559 4123661 lateral wash Allen Canyon

92.2 3 648003 4125824 lateral wash Montezuma Creek

84.1 3 635458 4127339 lateral wash Recapture Creek

57.9 2 603144 4115670 lateral wash Lime Creek

52.4 2 601301 4111310 lateral wash Gypsum Creek

17.7 2 575497 4130142 lateral canyon Slickhorn Canyon

16.4 1 573427 4130259 lateral canyon river right

10.0 1 563449 4126456 lateral canyon Buckhorn Canyon

8.1 1 561124 4128666 lateral canyon Steer Gulch

3.3 1 553978 4127054 lateral wash river right

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Table A-4. Summary of age-0 fishes collected in the San Juan River during the 2017 larval fish survey. Effort = 12,358.8 m2.

TOTAL PERCENT FREQUENCY % FREQUENCY RESIDENCE NUMBER OF OF OF OF SPECIES STATUS1 SPECIMENS TOTAL CPUE2 OCCURENCE3 OCCURENCE3

CARPS AND MINNOWS

Colorado Pikeminnow N 172 0.6 1.4 28 9.7 Common Carp I 82 0.3 0.7 18 6.2 Fathead Minnow I 876 2.9 7.1 44 15.2 Red Shiner I 263 0.9 2.1 43 14.9 Roundtail Chub N - - - - - Speckled Dace N 10,142 33.5 82.1 115 39.8

SUCKERS

Bluehead Sucker N 12,624 41.7 102.1 119 41.2 Flannelmouth Sucker N 4,751 15.7 38.4 128 44.3 Razorback Sucker N 360 1.2 2.9 37 12.8 White Sucker I 12 * 0.1 2 0.7

BULLHEAD CATFISHES

Black Bullhead I 19 0.1 0.2 3 1.0 Channel Catfish I 203 0.7 1.6 22 7.6 Yellow Bullhead I - - - - -

KILLIFISHES

Plains Killifish I 17 0.1 0.1 9 3.1

LIVEBEARERS

Western Mosquitofish I 685 2.3 5.5 86 29.8

SUNFISHES

Bluegill I 2 * * 1 0.3 Green Sunfish I 4 * * 4 1.4 Largemouth Bass I 27 0.1 0.2 14 4.8

TOTAL 30,239 244.7

1 N = native; I = introduced 2 CPUE = catch per unit effort; value based on catch per 100 m2 (surface area) sampled 3 Frequency and % frequency of occurrence are based on n = 289 samples. * Value is less than 0.05%

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Table A-5. Summary of age-1+ fishes collected in the San Juan River during the 2017 larval fish survey. Effort = 12,358.8 m2.

TOTAL PERCENT FREQUENCY % FREQUENCY RESIDENCE NUMBER OF OF OF OF SPECIES STATUS1 SPECIMENS TOTAL CPUE2 OCCURENCE3 OCCURENCE3

CARPS AND MINNOWS

Colorado Pikeminnow N 233 17.3 1.9 62 21.5 Common Carp I 4 0.3 * 4 1.4 Fathead Minnow I 136 10.1 1.1 30 10.4 Red Shiner I 219 16.2 1.8 51 17.6 Roundtail Chub N - - - - - Speckled Dace N 289 21.4 2.3 63 21.8

SUCKERS

Bluehead Sucker N 12 0.9 0.1 7 2.4 Flannelmouth Sucker N 135 10.0 1.1 15 5.2 Razorback Sucker N - - - - - White Sucker I - - - - -

BULLHEAD CATFISHES

Black Bullhead I 2 0.1 * 2 0.7 Channel Catfish I 14 1.0 0.1 6 2.1 Yellow Bullhead I - - - - -

KILLIFISHES

Plains Killifish I 7 0.5 0.1 6 2.1

LIVEBEARERS

Western Mosquitofish I 294 21.8 2.4 51 17.6

SUNFISHES

Bluegill I - - - - - Green Sunfish I 1 0.1 * 1 0.3 Largemouth Bass I 2 0.1 * 2 0.7

TOTAL 1,348 10.9

1 N = native; I = introduced 2 CPUE = catch per unit effort; value based on catch per 100 m2 (surface area) sampled 3 Frequency and % frequency of occurrence are based on n = 266 samples.  Value is less than 0.05%

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Scientific Name Common Name Code

Order Cypriniformes Family Cyprinidae carps and minnows

Cyprinella lutrensis...... Red Shiner (CYPLUT) Cyprinus carpio...... Common Carp (CYPCAR) Gila robusta...... Roundtail Chub (GILROB) Pimephales promelas...... Fathead Minnow (PIMPRO) Ptychocheilus lucius...... Colorado Pikeminnow (PTYLUC) Rhinichthys osculus...... Speckled Dace (RHIOSC)

Family Catostomidae suckers

Catostomus commersonii……………...... White Sucker (CATCOM) Catostomus (Pantosteus) discobolus...... Bluehead Sucker (CATDIS) Catostomus latipinnis...... Flannelmouth Sucker (CATLAT) Xyrauchen texanus...... Razorback Sucker (XYRTEX)

Order Siluriformes Family Ictaluridae catfishes

Ameiurus melas...... Black Bullhead (AMEMEL) Ameiurus natalis*...... Yellow Bullhead (AMENAT) Ictalurus punctatus...... Channel Catfish (ICTPUN)

Order Cyprinodontiformes Family Fundulidae topminnows

Fundulus zebrinus...... Plains Killifish (FUNZEB)

Family Poeciliidae livebearers

Gambusia affinis ...... Western Mosquitofish (GAMAFF)

Order Perciformes Family Centrarchidae sunfishes

Lepomis cyanellus...... Green Sunfish (LEPCYA) Lepomis macrochirus*...... Bluegill (LEPMAC) Micropterus salmoides...... Largemouth Bass (MICSAL)

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Table A-7. Covariates used in mixture models for Razorback Sucker.

Covariate Description Year The calendar year in which the larval survey took place. Reach Each of the 5 geomorphic reaches (5–1) within the study area. Mean March, April and May Daily mean temperature data was taken from USGS gage temperature #09379500 near Bluff, Utah. Mean March, April and May Daily mean discharge data (cfs) was taken from USGS gage discharge #09379500 near Bluff, Utah. Annual # stocked The number of Razorback Sucker stocked within a calendar year. Fish stocked in a given year were used as a covariate for larval captures during the following larval survey year (i.e. 1+ overwinter periods). Cumulative # stocked The number of Razorback Sucker stocked during the time period between 1998 and the year prior to the larval survey year. (e.g., 5,000 fish stocked between 1998–2000 would be used as a covariate for 2001 larval capture data). Fall monitoring captures All fall monitoring captures of adult Razorback Sucker. Fish collected during a given year were used as a covariate for larval captures during the following larval survey year (i.e. 1+ overwinter periods).

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Table A-8. Covariates used in mixture models for Colorado Pikeminnow.

Covariate Description Year The calendar year in which the larval survey took place. Reach Each of the 5 geomorphic reaches (5–1) within the study area. Mean June and July Daily mean temperature data was taken from USGS gage temperature #09379500 near Bluff, Utah. Mean June and July discharge Daily mean discharge data (cfs) was taken from USGS gage #09379500 near Bluff, Utah. Cumulative # stocked The number of age-0 Colorado Pikeminnow stocked during the time period between 1998 and five years prior to the larval survey year. (e.g., 100,000 fish stocked in 2000 would be used as a covariate for 2005 larval capture data). Fall monitoring captures 400+ All fall monitoring captures of Colorado Pikeminnow greater mm TL than 400 mm TL. Fish collected during a given year were used as a covariate for larval captures during the following larval survey year (i.e. 1+ overwinter periods).

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

APPENDIX B

Figure B-1 Densities by reach for Age-0 fish collected in the upper section (Farmington to Shiprock, NM). Reach 5 L is the area below Shiprock and Reach 5 U is the area above Shiprock. Species listed are the same (n = 9) as those tracked in the long- term larval fish dataset.

Colorado Pikeminnow densities by reach.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Razorback Sucker densities by reach.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Bluehead Sucker densities by reach.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Flannelmouth Sucker densities by reach.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Speckled Dace densities by reach.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Fathead Minnow densities by reach.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Red Shiner densities by reach.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Common Carp densities by reach.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Channel Catfish densities by reach.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Response to reviewers’ comments

Reviewer: Dr. Wayne Hubert

The PIs have produced a very thorough, readable report of the larval fish sampling efforts. Without getting into very specific comments regarding minuscule points on sentence structure, alternative wording, and the construction of figures and tables, little constructive criticism can be provided. However, I have one nagging sampling issue that bothers me. I wonder if the numbers of sampling trips are adequate to represent effectively the densities, as well as the spatial and temporal distributions, of Colorado Pikeminnow and Razorback Sucker within each year. This is especially true during years when sampling efficiency during some sampling periods is affected by high discharge. I think it would be wise for the PIs to consider potential biases that may be occurring in estimates of densities, descriptions of spatial and temporal distributions, and back calculations of spawning times of the endangered species due to limited numbers of sampling trips. I recognize how budget limitations constrain the number of sampling trips, but it would be good to recognize the data limitations and potential bias or errors in various estimates that result from a small number of sampling events. Understanding possible errors would be useful in the interpretation of annual results and assessment of temporal trends. I would like to see the inclusion of some discussion regarding this concern.

Response: Dr. Hubert raises several valid points. We have tried to give careful consideration to these concerns. Additional sampling could potentially improve the interpretation of the larval fish monitoring results, but that additional effort would have to be very specific and targeted, depending on which species we are looking at.

For example, larval Colorado Pikeminnow have not been collected in the San Juan River prior to the month of July. When considering what data should go into our mixture-model analysis, we include only July and August data. Our sampling efforts were further refined when an examination of the data determined 99.9% of larval Colorado Pikeminnow collected during the tenure of the study had been collected during the month of July. So sampling for Colorado Pikeminnow now consistently takes place during the second and fourth weeks in July. We feel the consistency in the timing of the sampling efforts allows for a meaningful interpretation of the duration and magnitude of Colorado Pikeminnow spawning in the San Juan River. It is recognized that any monitoring program will likely benefit from larger sample sizes and increases in sampling efforts. However, a programmatic discussion was had regarding the feasibility of sampling for Colorado Pikeminnow for four consecutive weeks in July, but it was determined to be unfeasible.

A similar situation exists for Razorback Sucker. Because spawning by Razorback Sucker occurs over a substantially longer time period (i.e. months), sampling efforts target the emergence of larvae (April), peak occurrence (May) and diminishing occurrence with later ontogenetic stages present (June). The two July sampling efforts have produced so few age-0 Razorback Sucker they are omitted from the mixture- model analysis. Razorback Sucker captured in July are included in back-calculated spawning dates, and distributional analysis. Again, it is acknowledged that additional sampling efforts would be beneficial, but we maintain that the consistency of sampling efforts, (monthly timing, amount of habitat sampled, and composition of different nursery habitats sampled) allow for a robust analysis of annual trends.

Finally in acknowledging the benefits of increasing sample size, for the past five years the contents of each seine haul has been preserved individually. Prior to 2013, the contents of all fish collected from a mesohabitat were preserved as a “site”. This change in protocol has increased the number of density estimates examined in any given year. For example, during the 2017 survey 1,130 individual density values were used in the mixture-model analysis done for the two endangered species; the number of sites sampled during 2017 was 289.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Reviewer: Dr. Stephen T. Ross

Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017.

Michael A. Farrington, Robert K. Dudley, Jennifer L. Kennedy, Steven P. Platania and Gary C. White

Congratulations on an excellent report. The amount of information on abundance, distribution, and habitat use of larval fishes is impressive and could readily form the basis of at least several journal articles. In particular, the long-term fluctuations of abundance of both native and nonnative fishes would make a very important contribution to the understanding fish assemblage dynamics in a western, managed river system. The patterns shown by Flannelmouth and Bluehead suckers are encouraging in that there is no evidence of a continual decline; however, as alluded to above, there are clearly some drivers of larval abundance that could be investigated in more detail.

Specific comments:

Lines 347 & 359. Start off these paragraphs with a clear statement about the biological meaning of your analyses. Unless the readers are familiar with modeling (which is generally not true), they aren’t going to gain much understanding about drivers of larval fish abundance from the executive summary.

Response: Changes made.

Lines 561-562. Indicate what the orange circles denote in Figure 1.

Line 581. I would find it helpful if you indicated the monitoring sites on a map.

Response: A new map that addresses both of the above comments is now in the Final Report

Line 708. No period after et in et al.

Response: Changes made.

756-758. “Thus, the autumnal abundance of adult Colorado Pikeminnow explained most of the variation in larval fish densities recorded the following summer.” This is exactly the kind of biologically meaningful statement that needs to be included in your analyses- thanks!

Line 951. Figure 5. Can this be moved closer to page 9?

Response: The figure has been moved closer to page 9.

Figures 7, 14 & 21. There are no labels on the y-axes.

Response: The figures now have labels on the y-axes.

Line 1000. Add a general statement of biological meaning similar to what you did for Colorado Pikeminnow (lines 756-758).

Response: An additional statement has been added to the end of the previous paragraph.

Line 1009. Don’t you mean that age-0 fish (not adults) are becoming more abundant?

Response: While true that age-0 fish are becoming more abundant, the statement is meant to suggest adults are as well. The reasoning behind the statement builds upon data reported in the 2016 Long term monitoring of sub-adult and adult large-bodied fishes. This has been clarified, and the appropriate citation included in the Final Report.

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Colorado Pikeminnow and Razorback Sucker larval fish survey in the San Juan River during 2017. Final Report American Southwest Ichthyological Researchers, L.L.C. 28 June 2018

Lines 1037-1039. “Densities of larval Razorback Sucker were highest in Reach 1 (8.9) and lowest in Reach 6 (0.07) [Figures 7 and B-1]). This pattern of increasing larval Razorback Sucker densities from upstream to downstream has been observed throughout the tenure of this study.” Along with the genetics data showing separation of sibs, this statement suggests to me that it is extremely likely that age-0 Razorback Suckers are moving downstream and many likely end up in Lake Powell.

Response: We agree. It is hoped that the sampling of larval fishes below the Paiute Farms waterfall, and the inclusion of any age-0 Razorback Sucker collected into the ongoing Nb work being conducted, will provide additional information on Razorback larvae that may end up in Lake Powell.

Lines 1160. Bluehead Suckers seem to be showing a sinusoidal pattern of abundance. Perhaps this is driven by spring discharge magnitudes. A quick look at discharge data from USGS gauge at Shiprock suggests that peaks in Bluehead Sucker numbers in 2004 & 2012 coincided with low spring discharge peaks, whereas the low numbers in 2003 & 2009 occurred during a years with stronger peaks in spring discharge. I don’t know if this would hold up to serious scrutiny but it might be worth examining. The effect of high spring peaks could be increased downstream transport into Lake Powell, or increased mortality caused directly or indirectly by depressed water temperatures. In the Discussion you also make this point for Razorback Suckers and Colorado Pikeminnow.

Response: Bluehead Sucker larvae would presumably be subjected to the same displacement and mortality as both the endangered species. It is interesting that the timing of Bluehead Sucker spawning tends to mimic that of Colorado Pikeminnow more so than Razorback Sucker (i.e. spawning activities peak post spring runoff). As noted in the Discussion, even moderate discharge rates were shown to displace larval Colorado Pikeminnow throughout the entire reach of critical habitat in a matter of days. I see no reason larval Bluehead Sucker would be any different. One approach to testing this would be the inclusion of flow covariates to the mixture-models being done for Bluehead Sucker.

Line 1168. The abundance estimates over time for Flannelmouth Suckers and for Red Shiners look very similar to population trajectories where there is a boom period, perhaps due to abundant resources/lower competition or something else, followed by a bust, perhaps due to increased intraspecific competition. Your data show very interesting patterns!

Response: Thank you.

Line 1546, Upper Reach Sampling. Age-0 fish collected in the upper reach sampling made up 66.8% of the total number of age-0 fish collected in the entire study. However, only three Colorado Pikeminnow and one Razorback Sucker were collected. The study showed that there is larval production in this more upstream area, but so far your data may indicate that this upstream reach is not a major spawning area. You say a little about this in the Discussion, but you do not address the issue of whether or not sampling should continue in this reach. [I think it should be, given that you shift to a more standardized sampling regime.]

Response: For a variety of reasons, the objectives for this project are being modified to target the collection of larval Colorado Pikeminnow only. Future sampling efforts will be confined to a single pass annually, and it is anticipated sampling of this river reach will be phased out.

Lines 1642 & 1749 Correct spelling (Schleicher not Schleichler).

Response: Changes made. My apologies to Benjamin Schleicher.

Lines 1673-1676. You indicate the goals for the upstream reach, but don’t say anything specific about what you found (see previous comment).

Response: It was felt that because the project had a single year of data, it would be difficult to draw definitive conclusions on what that data meant. Therefore we presented density data that can be

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However, the contrast of the data collected in 2017 (a high discharge year) and the data currently being collected in 2018 (a very low discharge year) will be included in the 2018 report.

Line 1841. No italics for Copeia.

Response: Changes made.

Lines 1914-1915. Separate the two references: Minckley, W. L. 1973. Fishes of Arizona. Phoenix: Arizona Game and Fish Department.

Moore, D. S. 1995. The basic practice of statistics. NY: Freeman and Co

Response: Changes made.

Reviewer: Matthew P. Zeigler

It might be worth pointing out that some proportion of the age-1 CPM captured in 2017 were likely wild.

Response: It is now noted that because 2016 was a strong reproductive year for Colorado Pikeminnow that was documented by both the larval and small-bodied monitoring programs, some proportion of the 2017 age-1 fish capture were likely wild individuals

Additional editorial comments made by the reviewer were corrected in the Final Report.

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