san joaquin river water quality …...san joaquin river h. t. harvey & associates water quality...

7815 North Palm Avenue, Suite 301 ● Fresno, California 93711 ● Ph: 559.476.3160 ● F: 559.476.3170

SAN JOAQUIN RIVER WATER QUALITY IMPROVEMENT PROJECT

PHASE I 2012 WILDLIFE MONITORING REPORT

Prepared by:

H. T. Harvey & Associates

Prepared for:

San Luis and Delta Mendota Water Authority Grassland Basin Drainers

c/o Joseph C. McGahan Summers Engineering

P.O. Box 1122 Hanford, CA 93232

Project #1960-14 October 2013

SJRIP Egg Mean Selenium Levels

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San Joaquin River H. T. Harvey & Associates Water Quality Improvement Project i October 2013 2012 Wildlife Monitoring Report

Executive Summary

This report presents the results of the twelfth year of biological monitoring for Phase I of the San Joaquin River Water Quality Improvement Project (SJRIP). The SJRIP is designed to reduce the amount of salt and selenium delivered to the San Luis Drain and Mud Slough through the Grassland Bypass. At this point in the project, approximately 5138 acres of the project site have been planted with salt-tolerant crops and irrigated with agricultural drainwater. The majority (4035 acres) of the salt tolerant crops are within 4095 acres, hereafter referred to as the eastern project area because they are situated east of Russell Avenue near the city of Firebaugh, in Fresno County, California. An additional 1861 acres acquired in 2008 were planted with 1103 acres of salt-tolerant crops. These 1861 acres are hereafter referred to as the western project area because they are located west of Russell Avenue. In 2012, avian monitoring was continued, and included evaluation of bird use of the eastern and western project areas; the numbers and nesting outcomes of killdeer (Charadrius vociferus), black-necked stilts (Himantopus mexicanus), and American avocets (Recurvirostra americana); and the selenium, boron, and mercury content of eggs of killdeer, black-necked stilts, American avocets, and red-winged blackbirds (Agelaius phoeniceus) nesting in the project areas, a mitigation site, and a reference area outside the project site. In addition, a tiered program for monitoring contaminants, designed to detect potential exposure of San Joaquin kit foxes (Vulpes macrotis mutica) to selenium by monitoring selenium levels in vegetation and small mammals, was conducted for the fifth year in the eastern and western project areas. An ornithologist from H. T. Harvey & Associates monitored bird use of the eastern and western project areas on 6 occasions between 30 April and 18 June 2012. The diversity of avian species detected and the number of individuals observed on the eastern project area has remained relatively low since avian counts began in 2003. To protect shorebirds from project-related impacts, measures have been implemented since 2006 to discourage shorebirds from foraging and nesting on the project site. The Panoche Drainage District has hazed shorebirds from the project site, modified open drains to deter shorebirds from using traditional nest sites, and installed a mitigation site to provide an alternative clean-water nesting habitat. To further prevent nesting within the project site, a total of 7.5 miles (mi) of drain have been filled and 3.4 mi have been reduced in size since 2006. In the eastern project area in 2012, habitat modifications combined with hazing reduced shorebird nesting to zero nest attempts for recurvirostrids (black-necked stilt and American avocet, combined) and to 10 nest attempts for killdeer. Only one killdeer and no recurvirostrids were detected nesting in the western project area in 2012. Eggs were collected for each of 3 avian species groups: 7 killdeer and 11 red-winged blackbird eggs were collected from the eastern project area (there were no recurvirostrid nests in the eastern project area); 5 recurvirostrid eggs were collected from the mitigation site; and 10 killdeer, 10 recurvirostrid, and 11 red-

San Joaquin River H. T. Harvey & Associates Water Quality Improvement Project ii October 2013 2012 Wildlife Monitoring Report

winged blackbird eggs were collected from the reference area. All collected eggs were analyzed for selenium, boron, and mercury concentrations. Eggs from the reference area provided data on the local “background” concentrations of selenium, boron, and mercury. Nearly all analyzed eggs contained at least partially elevated selenium concentrations. The geometric mean egg-selenium concentrations from the eastern project area were: 20.2 parts per million (ppm) for killdeer and 9.0 ppm for red-winged blackbirds. For the reference samples, the geometric mean egg-selenium concentrations were 7.0 ppm, 10.9 ppm, and 4.3 ppm for killdeer, recurvirostrids, and red-winged blackbirds, respectively. The mean selenium levels in eggs collected from the eastern project area were significantly higher than those from the reference area in both killdeer and red-winged blackbirds. The geometric mean selenium concentration of recurvirostrid eggs from the mitigation site was 5.4 ppm. The boron analysis of eggs collected from the eastern project area revealed that red-winged blackbirds had egg boron concentrations above the 3 ppm dry weight considered “background.” The geometric mean egg-boron concentrations from the eastern project area were 1.7 ppm for killdeer and 8.1 ppm for red-winged blackbirds. Reference area egg-boron concentrations were 0.6 ppm for killdeer, 1.5 ppm for recurvirostrids, and 1.0 ppm for red-winged blackbirds. There was no significant difference between mean boron levels in eggs collected from the mitigation site and eggs collected from the reference area for recurvirostrids in 2012, although there was a significant difference in this value for killdeer and red-winged blackbird eggs: mean boron levels were significantly higher in the eastern project area. Eggs collected were analyzed for mercury for the fourth year in 2012. All of the eggs sampled from the project area and mitigation sites were within published recommended guidelines for egg-mercury concentrations (<0.5 ppm wet weight). The geometric mean egg-mercury concentrations (wet weight) from the eastern project area were 0.122 ppm for killdeer and 0.024 ppm for red-winged blackbirds. Reference area egg-mercury concentrations were 0.081 ppm for killdeer, 0.216 ppm for recurvirostrids, and 0.015 ppm for red-winged blackbirds. There was a significant difference in mean mercury levels between eggs collected from the eastern project area and eggs collected from the reference area for killdeer and for red-winged blackbirds: mean mercury levels were significantly higher in the eastern project area. Results of the Tiered Contaminant Monitoring Program included geometric means of 3.18 ppm selenium in vegetation and 3.30 ppm in small mammals collected from the eastern project area, 1.65 ppm selenium in vegetation and 2.98 ppm in small mammals from fields in the western project area that received at least some drainwater, and 1.20 ppm selenium in vegetation and 2.38 ppm in small mammals from fields in the western project area that received no drainwater. The selenium levels detected in 8 of 21 vegetation samples and in 9 of 21 small mammal samples exceeded the threshold of 3 ppm recommended by the U.S. Fish and Wildlife Service as the upper limit of long-term dietary exposure for mammals.

San Joaquin River H. T. Harvey & Associates Water Quality Improvement Project iii October 2013 2012 Wildlife Monitoring Report

Table of Contents

Executive Summary ............................................................................................................................................................. i Table of Contents .............................................................................................................................................................. iii Section 1.0 Introduction ............................................................................................................................................. 1

1.1 Project Description and Setting ............................................................................................................................ 1 1.1.1 Monitoring History and Mitigation Measures ............................................................................................ 5

Section 2.0 Materials and Methods ........................................................................................................................... 8 2.1 Bird Censuses ........................................................................................................................................................... 8 2.2 Egg Collection and Processing .............................................................................................................................. 8

2.2.1 Egg Chemistry Analysis ................................................................................................................................ 14 2.2.2 Analyses of 2012 Data .................................................................................................................................. 14 2.2.3 Analyses across Years ................................................................................................................................... 14

2.3 Nest Fate ................................................................................................................................................................. 16 2.4 Mitigation Site Water Quality .............................................................................................................................. 16 2.5 Tiered Contaminant Monitoring Program ........................................................................................................ 16

2.5.1 Vegetation Sampling ..................................................................................................................................... 17 2.5.2 Small Mammal Sampling .............................................................................................................................. 17 2.5.3 Plant and Small Mammal Chemistry Analysis .......................................................................................... 19

Section 3.0 Results ..................................................................................................................................................... 20 3.1 Bird Censuses ......................................................................................................................................................... 20 3.2 Egg Collection and Processing ............................................................................................................................ 20 3.3 Egg-Selenium Analysis ......................................................................................................................................... 29

3.3.1 2012 Egg-Selenium Data Analysis between Sites ..................................................................................... 29 3.3.2 Egg-selenium Data Analysis across Years ................................................................................................. 29 3.3.3 Recurvirostrid Mitigation Site Selenium Concentrations ........................................................................ 37

3.4 Egg-boron Analysis ............................................................................................................................................... 38 3.4.1 2012 Egg-boron Data Analysis between Sites .......................................................................................... 38 3.4.2 Egg-boron Data Analysis across Years ...................................................................................................... 38 3.4.3 Recurvirostrid Mitigation Site Boron Concentrations ............................................................................. 46

3.5 Egg-mercury Analysis ........................................................................................................................................... 47 3.5.1 2012 Egg-mercury Data Analysis between Sites ...................................................................................... 47 3.5.2 Recurvirostrid Mitigation Site Mercury Concentrations ......................................................................... 47

3.6 Control Eggs .......................................................................................................................................................... 48 3.7 Nest Fate ................................................................................................................................................................. 49 3.8 Mitigation Site Water Quality .............................................................................................................................. 49 3.9 Tiered Biological Monitoring Program .............................................................................................................. 50

3.9.1 Vegetation Sampling and Selenium Analysis ............................................................................................ 50 3.9.2 Small Mammal Sampling and Selenium Analysis ..................................................................................... 52

Section 4.0 Discussion............................................................................................................................................... 55 Section 5.0 Literature Cited ...................................................................................................................................... 57

San Joaquin River H. T. Harvey & Associates Water Quality Improvement Project iv October 2013 2012 Wildlife Monitoring Report

Figures Figure 1. Site Vicinity Map—San Joaquin River Water Quality Improvement Project ............................. 3 Figure 2. San Joaquin River Water Quality Improvement Project Site Map ............................................... 4 Figure 3. Mitigation Site—San Joaquin River Water Quality Improvement Project .................................. 7 Figure 4. Project Site Killdeer Egg Collection Sites (2012) ............................................................................. 9 Figure 5. Project Site Red-winged Blackbird Egg Collection Sites (2012) ................................................. 10 Figure 6. Reference Area Killdeer Egg Collection Sites (2012).................................................................... 11 Figure 7. Reference Area Recurvirostrid Egg Collection Sites (2012) ........................................................ 12 Figure 8. Reference Area Red-winged Blackbird Egg Collection Sites (2012) .......................................... 13 Figure 9. Location of Vegetation Samples Collected and Small Mammals Trapped in 2012 ................. 18 Figure 10. Mean ± 95% Confidence Interval Egg-selenium Concentrations for Killdeer at the San

Joaquin River Water Quality Improvement Project (2002 to 2012) ........................................... 30 Figure 11. Predicted Egg-selenium Concentrations with 95% Confidence Bands for Killdeer at the San

Joaquin River Water Quality Improvement Project (2002 to 2012) ........................................... 32 Figure 12. Mean ± 95% Confidence Interval Egg-selenium Concentrations for Recurvirostrids at the

San Joaquin River Water Quality Improvement Project (2003 to 2012) ................................... 33 Figure 13. Predicted Egg-selenium Concentrations with 95% Confidence Bands for Recurvirostrids at

the San Joaquin River Water Quality Improvement Project (2003 to 2012) ............................. 34 Figure 14. Mean ± 95% Confidence Interval Egg-selenium Concentrations for Red-winged Blackbirds

at the San Joaquin River Water Quality Improvement Project (2003 to 2012) ........................ 35 Figure 15. Predicted Egg-selenium Concentrations with 95% Confidence Bands for Red-winged

Blackbirds at the San Joaquin River Water Quality Improvement Project (2003 to 2012) .... 36 Figure 16. Mean ± 95% Confidence Interval Egg-selenium Concentrations for Recurvirostrids at the

San Joaquin River Water Quality Improvement Project (2012) .................................................. 37 Figure 17. Mean ± 95% Confidence Interval Egg-boron Concentrations for Killdeer at the San Joaquin

River Water Quality Improvement Project (2002 to 2012) .......................................................... 39 Figure 18. Predicted Egg-boron Concentrations with 95% Confidence Bands for Killdeer at the San

Joaquin River Water Quality Improvement Project (2002 to 2012) ........................................... 41 Figure 19. Mean ± 95% Confidence Interval Egg-boron Concentrations for Recurvirostrids at the San

Joaquin River Water Quality Improvement Project (2003 to 2012) ........................................... 42 Figure 20. Predicted Egg-boron Concentrations with 95% Confidence Bands for Recurvirostrids at the

San Joaquin River Water Quality Improvement Project (2003 to 2012) (Note that Location Was Not a Significant Effect in the Model) ................................................................................... 43

Figure 21. Mean ± 95% Confidence Interval Egg-boron Concentrations for Red-winged Blackbirds at the San Joaquin River Water Quality Improvement Project (2003 to 2012) ............................. 44

Figure 22. Predicted Egg-boron Concentrations with 95% Confidence Bands for Red-winged Blackbirds at the San Joaquin River Water Quality Improvement Project (2003 to 2012) .... 45

Figure 23. Mean ± 95% Confidence Interval Egg-boron Concentrations for Recurvirostrids at the San Joaquin River Water Quality Improvement Project (2012) ......................................................... 46

Figure 24. Mean ± 95% Confidence Interval Egg-mercury Concentrations for Recurvirostrids at the San Joaquin River Water Quality Improvement Project (2012) .................................................. 48

San Joaquin River H. T. Harvey & Associates Water Quality Improvement Project v October 2013 2012 Wildlife Monitoring Report

Tables Table 1. Avian Census Results in the Eastern Project Area—San Joaquin River Water Quality

Improvement Project ......................................................................................................................... 21 Table 2. Avian Census Results in the Western Project Area—San Joaquin River Water Quality

Improvement Project ......................................................................................................................... 22 Table 3. Eastern Project Area Killdeer Egg-selenium Concentrations—San Joaquin River Water

Quality Improvement Project ........................................................................................................... 23 Table 4. Eastern Project Area Red-winged Blackbird Egg-selenium Concentrations—San Joaquin

River Water Quality Improvement Project ..................................................................................... 24 Table 5. Reference Area Killdeer Egg-selenium Concentrations—San Joaquin River Water Quality

Improvement Project ......................................................................................................................... 25 Table 6. Reference Area Recurvirostrid Egg-selenium Concentrations—San Joaquin River Water

Quality Improvement Project ........................................................................................................... 26 Table 7. Reference Area Red-winged Blackbird Egg-selenium Concentrations—San Joaquin River

Water Quality Improvement Project ............................................................................................... 27 Table 8. Mitigation Site Recurvirostrid Egg-selenium Concentrations—San Joaquin River Water

Quality Improvement Project ........................................................................................................... 28 Table 9. 2012 Geometric Mean Egg-selenium Concentrations—San Joaquin River Water Quality

Improvement Project ......................................................................................................................... 29 Table 10. Effects of Location and Year on Egg-selenium Concentrations in Killdeer (2002 to 2012),

and Recurvirostrids and Red-winged Blackbirds (2003 to 2012)—San Joaquin River Water Quality Improvement Project ........................................................................................................... 31

Table 11. 2012 Geometric Mean Egg-boron Concentrations—San Joaquin River Water Quality Improvement Project ......................................................................................................................... 38

Table 12. Effects of Location and Year on Egg-boron Concentrations in Killdeer, Recurvirostrids, and Red-winged Blackbirds (2003 to 2012)—San Joaquin River Water Quality Improvement Project ................................................................................................................................................... 40

Table 13. 2012 Geometric Mean Egg-mercury Concentrations—San Joaquin River Water Quality Improvement Project ......................................................................................................................... 47

Table 14. Nest Fates and Agents that Caused Nest/Clutch Success or Failure in the Eastern Project Area and Mitigation Site in 2012—San Joaquin River Water Quality Improvement Project 49

Table 15. Water Quality in Samples Taken from the Mitigation Site on 2 June 2012—San Joaquin River Water Quality Improvement Project ..................................................................................... 50

Table 16. Project Site Plant-selenium Concentrations—San Joaquin River Water Quality Improvement Project ................................................................................................................................................... 51

Table 17. 2012 Vegetation Selenium Concentrations by Crop Type and Location—San Joaquin River Water Quality Improvement Project ........................................................................................................... 52

Table 18. Small Mammal–Selenium Concentrations—San Joaquin River Water Quality Improvement Project ................................................................................................................................................... 53

San Joaquin River H. T. Harvey & Associates Water Quality Improvement Project vi October 2013 2012 Wildlife Monitoring Report

Appendices Appendix A. Examination of Residuals for Final Statistical Models ................................................................. 59 Appendix B. 2012 Killdeer Egg-boron Concentrations at the San Joaquin River Water Quality

Improvement Project ......................................................................................................................... 68 Appendix C. 2012 Recurvirostrid Egg-boron Concentrations at the San Joaquin River Water Quality

Improvement Project ......................................................................................................................... 70 Appendix D. 2012 Red-winged Blackbird Egg-boron Concentrations at the San Joaquin River Water

Quality Improvement Project ........................................................................................................... 72 Appendix E. 2012 Killdeer Egg-mercury Concentrations at the San Joaquin River Water Quality

Improvement Project ......................................................................................................................... 74 Appendix F. 2012 Recurvirostrid Egg-mercury Concentrations at the San Joaquin River Water Quality

Improvement Project ......................................................................................................................... 76 Appendix G. 2012 Red-winged Blackbird Egg-mercury Concentrations at the San Joaquin River Water

Quality Improvement Project ........................................................................................................... 78 Appendix H. 2012 Control Eggs, Selenium Results .............................................................................................. 80 Appendix I. 2012 Control Eggs, Boron Results ................................................................................................... 82 Appendix J. 2012 Control Eggs, Mercury Results ............................................................................................... 85 Appendix K. Killdeer and Recurvirostrid Nest Survey Results for the San Joaquin River Water Quality

Improvement Eastern Project Area and Pilot Mitigation Sites ................................................... 87 Contributors Scott B. Terrill, Ph.D., Principal-in-charge/Senior Ornithologist Brian B. Boroski, Ph.D., Principal/Senior Wildlife Ecologist Jeff L. Seay, B.A., Senior Wildlife Ecologist David Zajanc, M.A., Wildlife Ecologist

San Joaquin River H. T. Harvey & Associates Water Quality Improvement Project 1 October 2013 2012 Wildlife Monitoring Report

Section 1.0 Introduction

To reduce the amount of salt and selenium delivered to the San Luis Drain and Mud Slough through the Grassland Bypass Project, the San Luis and Delta Mendota Water Authority Grassland Basin Drainers implemented Phase I of the San Joaquin River Water Quality Improvement Project (SJRIP). The Panoche Drainage District, acting as the lead agency under the California Environmental Quality Act (CEQA), prepared a Negative Declaration for the SJRIP in September 2000. The Negative Declaration included a provision for the development, in collaboration with the U.S. Fish and Wildlife Service (Service), of a biological monitoring program that would detect potential project-related impacts on migratory birds resulting from exposure to elevated levels of selenium. This report represents the results of biological monitoring for the twelfth year (2012) of Phase I of the SJRIP. Also, the Final Biological Opinion for the Grasslands Bypass Project, October 1, 2001–December 31, 2009 (BO) stipulates that a monitoring program and contingency plan be designed, in consultation with the Service, to address potential San Joaquin kit fox (Vulpes macrotis mutica) exposure to selenium at the SJRIP site. Consequently, a Tiered Contaminant Monitoring Program to measure selenium levels in constituents of the San Joaquin kit fox food chain was implemented in 2008. The BO was updated in 2009 to cover the period from 2010 through 2019. In addition to reporting on project-related impacts on birds, this report presents the results of the fifth year of the Tiered Contaminant Monitoring Program.

1.1 Project Description and Setting

The project site is located west of the city of Firebaugh, in Fresno County, California (Figure 1). The irregularly shaped site is bordered on the north by the Main Canal and on the south by the Delta-Mendota Canal. The western edge extends nearly to Fairfax Avenue (Figure 2). The original 4095 acres of the site is referred to as the eastern project area, situated just east of Russell Avenue. An additional area, acquired in 2008 for future inclusion in the project, is hereafter referred to as the western project area, and is located west of Russell Avenue (Figure 2). The SJRIP consists of the initial development of an In-Valley Treatment/Drainage Reuse Facility on up to 6200 acres of land in the Grassland Drainage Area (GDA), which includes irrigated lands within Panoche Drainage District, Pacheco Water District, Charleston Drainage District, Firebaugh Canal Water District, Broadview Water District, and Camp 13 Drainage District. These 6200 acres of GDA land constitute the project site and contain irrigated field crops and related irrigation ditches, drainage ditches, conveyance canals, and farm structures. The topography is nearly level to grade and flood/furrow irrigated. The highest elevation, of 164 feet (ft) above mean sea level, is found near the southeast corner of the property, whereas the lowest point, 136 ft above mean sea level, is found near a north-central point. Thus, the elevation change within the project site is approximately 28 ft. The shape of the property is irregular, conforming to the area’s


adjacent canals. Russell Avenue provides access to the property via a paved county road. Typical, improved farm roads provide access to the interior of the site. The reuse facility dedicates specific lands for the irrigation of salt-tolerant crops with subsurface drainwater to reduce drainwater volume; treat the concentrated drainwater to remove salt, selenium, and boron; and eventually dispose of the removed elements to prevent their discharge into the San Joaquin River. Implementation of the facility project is planned to occur in 3 phases:

• Phase I: Purchase land and plant salt-tolerant crops

• Phase II: Install subsurface drainage and collection systems and the initial treatment system

• Phase III: Complete construction of treatment removal and salt disposal systems In Phase I, which began in 2001, subsurface drainwater from the GDA is used to irrigate salt-tolerant crops on ideally situated land within the project site. Channels containing collected drainwater flow adjacent to this location, so water can easily be captured and placed on the land. Also, because this land is at the lowest elevation within the GDA, collected water can be applied without excessive pumping costs. Approximately 6000 acres had been purchased prior to 2012. Since 2001, approximately 5140 acres have been planted in crops and irrigated with water that otherwise would have been discharged into the San Joaquin River. Soil and water constituents in this project area are monitored to prevent irreversible soil changes and to protect groundwater from contamination. In Phase II of the SJRIP, the application of saline water to lands developed in Phase I will continue. Subsurface drainage systems will be installed to leach the land and maintain a favorable salt balance. The water percolating below the root zone will be captured in the drainage system and passed on to more salt-tolerant crops to concentrate minerals and to decrease the volume of drainwater produced. The remaining salt, selenium, and other constituents will be conveyed by water exiting the subsurface drainage systems. The final treatment phase of the SJRIP will remove the salt, selenium, and much of the other constituents, leaving water for beneficial uses, such as agriculture. The treatment system will be incorporated into the reuse system. The removed salt will be deposited into approved waste units. The Phase III treatment and removal process will further reduce salt and selenium discharges into the San Joaquin River, maximize improvements in water quality, and meet requirements of future water quality objectives. Each phase of the facility will significantly reduce the amount of drainwater discharged to the San Joaquin River.

Main CanalOutside CanalDelta Mendota Canal

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Sources: Esri, DeLorme, NAVTEQ, USGS, Intermap, iPC, NRCAN, EsriJapan, METI, Esri China (Hong Kong), Esri (Thailand), TomTom, 2013

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Source: Esri, DigitalGlobe, GeoEye, i-cubed, USDA, USGS, AEX, Getmapping, Aerogrid, IGN, IGP,swisstopo, and the GIS User Community

LEGEND2012 Swainson's Hawk Nest SitesDrains ClosedDrains Reduced in Size2012 Mitigation SiteEastern Project AreaWestern Project Area

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An Initial Study and Negative Declaration, adopted 9 September 2000 by the Panoche Drainage District, evaluated Phase I of the facility. Phases II and III were evaluated in the Grassland Bypass Project Environmental Impact Statement/Environmental Impact Report (EIS/EIR), finalized 25 May 2001, and in a BO issued by the Service on 27 September 2001. Phase I is independent, and its implementation does not obviate the consideration of alternatives to the larger project or project site. Even if progress on the In-Valley Treatment/Drainage Reuse Facility were to halt at Phase I, the drainage management alone would be valuable. In addition, the proposed cropping patterns can be reversed if later phases of the project are not implemented. The Panoche Drainage District acquired an additional 1861 acres of Phase I lands in 2008 (Figures 1 and 2); this land is located west of Russell Avenue, between the Main and Outside canals. Monitoring of avian numbers and the selenium content of bird eggs, vegetation, and small mammals on these 1861 acres began in 2008. As of 2012, 1103 acres of salt tolerant crops had been planted there. Fields in Sections 1, 31, 32, and 36 were at least partially irrigated with drainwater in 2012, while fields in Sections 4, 5, and 6 were not.

1.1.1 Monitoring History and Mitigation Measures

The Negative Declaration for the SJRIP included provisions for wildlife monitoring that would assess project-related impacts on wildlife. Also, mitigation measures could be applied if the monitoring program detected negative impacts. The SJRIP biological monitoring program began the first year drainwater was applied to the project in 2001 and consisted of collection of killdeer (Charadrius vociferus) eggs on the project site for selenium and boron analysis. Since then, the monitoring program has evolved in response to monitoring results and to comply with monitoring requirements in the BO. The collection of recurvirostrid (black-necked stilt [Himantopus mexicanus] and American avocet [Recurvirostra americana]) eggs from the project site and the collection of reference sample killdeer eggs for selenium and boron analysis, and a bi-monthly census of bird use of the project site during nesting season were added in 2002. Red-winged blackbird (Agelaius phoeniceus) was added to the species groups for egg selenium and boron analysis in 2003. The sample size of eggs collected for selenium and boron analysis from the three species groups, killdeer recurvirostrids, and red-winged blackbirds, was increased to 20 eggs from each group for both projects site and reference samples. In 2004, the sample size of eggs collected from each species group was adjusted based on power analyses of the 2003 egg-selenium results. The resulting sample sizes, 15 for killdeer, 17 for recurvirostrids and 11 for red-winged blackbirds were applied to both project and reference samples. A mitigation site was added to the project in 2006 and additional monitoring included the collection of a set of recurvirostrid eggs for selenium and boron analysis. Monitoring of nest success in both killdeer and recurvirostrids at the project site and recurvirostrids at the mitigation site was also added in 2006. In 2009 the Service requested the addition of mercury to the metals analyzed in birds eggs.


Based on the waterborne and egg-selenium levels found in the eastern project area, lethal and sublethal effects on waterbirds breeding at the project site are considered probable. From 2003 to 2005, selenium in water samples from the sources of drainwater used to irrigate the eastern project area ranged from 43 to 761 parts per billion (ppb) (Panoche Drainage District data). Such levels are well above the level of waterborne selenium (32 ppb) associated with a high probability of reduced hatchability and increased probability of teratogenesis (CH2MHill et al. 1993). Consistent with the water data, elevated egg-selenium levels have been found in both recurvirostrid and killdeer eggs from the eastern project area. Egg-selenium levels in both avian groups have been higher than in similar sets of reference eggs collected from the project vicinity. Annual geometric mean egg-selenium levels from recurvirostrid eggs have varied, but from 2003 to 2011, most means were also above the level (18 parts per million [ppm]) associated with an increased probability of reduced hatchability and teratogenesis. Beginning in 2006, 3 mitigation measures were implemented to reduce impacts on nesting shorebirds. The first measure consisted of dredging the bottoms of open drains that are consistently used by shorebirds, to eliminate potential feeding and nesting substrates and thereby deter birds from using the area. For the second measure, Panoche Drainage District personnel discharged cracker shells to discourage shorebird use where shorebird nesting had been concentrated in the past. These hazers patrolled the project site throughout the day to discourage birds from establishing nests. The third measure consisted of enhancing habitat for nesting shorebirds outside the project site at a location with clean (nonseleniferous) water. These measures were continued and enhanced in 2007. Several drains were filled in the northern portion of the eastern project area (Sections 2 and 3), where killdeer and recurvirostrid nesting had been concentrated in recent years, and drains that could not be filled were covered with netting to prevent bird use. Drain closure and netting measures were expanded into the southern portion of the eastern project area in 2008. To date, a total of 7.5 miles (mi) of drain have been filled, and 3.4 mi of drains have been re-contoured and reduced in size (Figure 2). To balance these deterrence measures, approximately 15 acres of improved shorebird breeding habitat, comprising nesting islands in cultivated rice, have been provided as mitigation since 2006. In 2012, the mitigation site was moved to a new location at the southern edge of a rice field south of the Main Canal and west of Fairfax Avenue (Figures 2 and 3). As in previous years, rice was not planted in the portion of the rice field designated for the mitigation site, to provide open wetland habitat more amenable to shorebird foraging and nesting. Seven long islands, similar in width to the interior contour dikes were built to provide nesting islands for shorebirds (Figure 3).

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LEGEND2012 Mitigation Site

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Figure 3: Mitigation Site

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In-Valley Treatment/ Drainage Reuse Facility2012 Biological Monitoring (1960-14)


Section 2.0 Materials and Methods

2.1 Bird Censuses

An ornithologist from H. T. Harvey & Associates monitored bird use at the project site on 6 occasions between 30 April and 18 June 2012. The ornithologist conducted censuses on these occasions to determine species composition and the relative abundance of bird species in the eastern and western project areas during the breeding season. Censuses were completed by driving the perimeter roads of each agricultural field on site and stopping frequently to observe birds. Birds were identified and counted using 10X binoculars and a 20–60X spotting scope mounted on a tripod.

2.2 Egg Collection and Processing

Seven killdeer eggs and 11 red-winged blackbird eggs were collected from the eastern project area for selenium, boron, and mercury analysis. No recurvirostrid nests were located in the eastern project area. The locations from which killdeer and red-winged blackbird eggs were collected from the eastern project area are illustrated in Figures 4 and 5; respectively. Scientific collecting permits were obtained from the California Department of Fish and Game (CDFG) and the Service for the collection of bird eggs on the site. One egg was randomly collected from separate, full-clutch nests (those with at least 4 eggs). Also, 10 reference killdeer eggs (Figure 6), 10 recurvirostrid eggs (Figure 7), and 11 red-winged blackbird eggs (Figure 8) were collected from the project vicinity to provide reference data on regional selenium, boron, and mercury concentrations outside the site. Reference area eggs were collected from the project vicinity on lands similar in character to the eastern project area. A one mile buffer around the eastern project area was imposed to reduce the likelihood of project effects on reference samples. Five recurvirostrid (3 black-necked stilt and 2 American avocet) eggs were also collected from the mitigation site for selenium, boron, and mercury analysis. Collected eggs were labeled with a permanent marker, and all of the egg contents, including membranes, were removed from the shell and transferred to 1-ounce Dynalon jars. Each embryo was examined for morphological abnormalities, and the stage of incubation was established using photographs of known-age embryos. The embryo was also examined to determine if it was alive or dead, and was photographed. The egg contents were then frozen for storage.

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Figure 4: Project Site Killdeer Egg Collection SitesOctober 2013

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Figure 5: Project Site Red-winged Blackbird Egg Collection SitesOctober 2013

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Figure 6: Reference Area Killdeer Egg Collection SitesOctober 2013

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Figure 7: Reference Area Recurvirostrid Egg Collection SitesOctober 2013

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LEGENDRed-winged Blackbird Egg Collection SitesWestern Project AreaEastern Project Area

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Figure 8: Reference Area Red-winged Blackbird Egg Collection SitesOctober 2013

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2.2.1 Egg Chemistry Analysis

All egg contents collected by H. T. Harvey & Associates were shipped overnight on dry ice to the South Dakota Agricultural Laboratories, a private enterprise headed by Regina Wixon, Ph.D. This laboratory was founded by former personnel of South Dakota State University’s Oscar E. Olson Biochemical Laboratory, which closed in 2011. We had used the Oscar E. Olson Biochemical Laboratory for egg-selenium analyses since 2003. At the laboratory, selenium concentrations were determined using the Association of Official Analytical Chemists method 996.16. Boron levels were quantitated using a nitric acid/peroxide digest in a microwave oven and an inductively coupled plasma optical emission spectrometer. All egg-selenium and egg-boron concentrations were presented in parts per million (ppm) based on dry tissue weight (dry weight). Whole mercury concentrations were determined using Cold Vapor Atomic Fluorescence Spectroscopy. Egg-mercury results were analyzed based on wet-weight values in parts per million (ppm) because wet weight is the format in which most published toxicity thresholds for eggs are presented. Egg-mercury results are also presented in parts per billion (ppb) dry weight. For quality control, selected subsamples were divided into 2 aliquots. The duplicate was spiked with known amounts of selenium, boron, or mercury, and the samples were tested to determine the accuracy of the analysis.

2.2.2 Analyses of 2012 Data

Statistics describing the chemical concentrations of selenium, boron, and mercury in sampled eggs from 2012 were calculated (geometric mean and range of raw data, and confidence intervals and means for log-transformed data), and the chemical concentrations in eggs were compared between the eastern project area and reference areas for killdeer and red-winged blackbirds. All chemical concentrations were log-transformed (log10[x+1], where x is the concentration) to homogenize variance as much as possible. We used one-way ANOVA to test for the effect of location (project and reference) on selenium, boron, and mercury concentrations in killdeer and red-winged blackbird eggs collected in 2012. For all tests conducted, a p-value of less than 5% (p<0.05) was considered significant, a p-value between 5% and 10% (0.05<p<0.10) was considered inconclusive, and a p-value greater than 10% (p>0.10) was considered not significant. We also used one-way ANOVA to compare chemical concentrations in mitigation site recurvirostrid eggs to those in reference recurvirostrid eggs; no recurvirostrid eggs were sampled from the eastern project area.

2.2.3 Analyses across Years

Linear models were used to evaluate egg-selenium and egg-boron concentrations with respect to location and time for killdeer based on data from 2002 to 2012, and recurvirostrids, and red-winged blackbirds, based on data from 2003 to 2012. Egg-selenium or egg-boron concentration was the dependent variable. Egg-selenium and egg-boron concentrations were log-transformed (log10[x+1], where x is the concentration) to homogenize variance as much as possible. For this year’s analysis of chemical concentrations in bird eggs, we evaluated whether there were trends in concentrations with time. This approach contrasts with previous


years’ analyses, which simply looked for differences in concentrations between years (by treating year as a factor). That approach was appropriate when there were fewer years of data, but with more years of data, a model that treats year as a factor results in an unwieldy number of variables and too many degrees of freedom, violating the principle of parsimony. Prior analyses established that chemical concentrations did often differ by year, but now we can evaluate longer-term trends. In addition to evaluating a simple linear trend with year, we evaluated polynomials of the second and third order for year. For models with a higher order polynomial term (i.e., quadratic or cubic polynomial), we assumed that all lower-order terms (i.e., 1st order for quadratic, 1st and 2nd order for cubic) also needed to be in the model; we evaluated the effect of dropping all year variables (e.g., for quadratic polynomial, both year and year2) when we quantified the statistical significance for the year effect. This approach was applied to interaction effects as well. For instance, for the location x year2 interaction (quadratic year term), we included lower-order interactions in the model as well (i.e., location x year); we evaluated the effect of dropping all interaction terms from the model when we quantified the statistical significance of the interaction effect. The process of model selection involved evaluating the violation of assumptions of a simple linear regression model and fitting alternate models if assumptions were violated. First, we fit a simple linear model with main effects location (nominal variable) and year (continuous variable), and interaction terms (i.e., full model). We then examined plots of the residuals to see if there were violations of the assumptions for the simple linear model, in other words, homoscedasticity, normality, and independence. Visual inspection of residuals is the method preferred by some (i.e., Zuur et al. 2009, p. 20) because of the sensitivities of available tests to non-normality, and is the method used for our analyses. If the assumptions were violated, alternate models were fitted. If heteroscedasticity was indicated (i.e., by some pattern in the residuals), we first attempted to use a weighted linear regression model that incorporates a variance structure based on covariates (i.e., year and/or site), a preferred method of accounting for heterogeneity (Zuur et al. 2009). If patterns in the residuals suggested a violation of independence (i.e., through an increasing spread with increasing fitted values), we examined an autocorrelation plot of the residuals; if this plot corroborated a violation of independence, a new model was fit that incorporated a temporal correlation structure. We used an autoregressive moving average (ARMA) structure for the temporal correlation (see Zuur et al. 2009 for details). If the assumptions of homoscedasticity and independence were met, and if the distribution of the residuals was clearly non-normal, we implemented a generalized linear model (GLM), which can account for a non-normal structure in error (McCullagh and Nelder 1989). We addressed issues of non-normality where possible, but where there were issues with violations of independence or heterogeneity, we prioritized addressing those issues first, because the consequences of these violations are more severe with respect to interpretation of test statistics and p-values. In addition, several authors (Sokal and Rohlf 1995; Zar 1999; Zuur et al. 2009) argue that, following the central limit theorem, non-normality is not critical within the context of regression analyses, assuming a reasonable sample size.


If the newly fit model was better than the original linear model in terms of error behavior (i.e., meeting the assumptions of homogeneity, normality, and independence) and model fit (i.e., based on Akaike information criterion [AIC] or likelihood ratio tests), we selected it as our final model. We then quantified the statistical significance of the effects of location, year, and the interaction between location and year, via comparison of nested models. For GLMs and linear regression models that incorporated variance or temporal correlation structure, we employed a likelihood ratio test to make the statistical comparisons, whereas for simple linear models, we used an F test. All statistical analyses were conducted in R (R Development Core Team 2013).

2.3 Nest Fate

In addition to egg-selenium monitoring, killdeer and recurvirostrid nests in the eastern project area and mitigation site were monitored to determine nest fate. Red-winged blackbird nests were not monitored after egg collection because it is not practical to relocate their nests multiple times without negatively affecting their fledging success. Active nests were located by conducting vehicle surveys for adult killdeer and recurvirostrids. Once located, adults were monitored with a spotting scope or binoculars until a nest location could be determined. Nests were located at the mitigation site by walking the levees and islands. Nest locations were marked using a Global Positioning System (GPS) unit (Garmin GPSmap 76CSx, 12 Channel, Olathe, KS). Nest location, stratum, date, number of eggs present, nest status, nest/clutch fate, and nest agent were recorded for each nest encountered. The nests were monitored to completion, and nest fates were recorded. A completed nest was one that was empty (chicks presumed to have hatched or a predator took the eggs), abandoned, destroyed, or one in which chicks were present.

2.4 Mitigation Site Water Quality

Water samples were collected from the inlet, center, and outlet of the mitigation site on 12 July 2012. The samples were sent to the Agriculture & Priority Pollutants Laboratories, Inc., in Clovis, California, to be analyzed for total dissolved solids, selenium, and boron content.

2.5 Tiered Contaminant Monitoring Program

The Tiered Contaminant Monitoring Program, initiated in 2008 to assess the potential for the project to contribute to selenium contamination of the federally listed threatened San Joaquin kit fox, continued as in the past, except that coyote hair and blood sampling has been discontinued. At a 12 September 2012 project meeting of the U.S. Bureau of Reclamation, the Service, and the Panoche Drainage District, it was agreed that the coyote portion of the monitoring would be suspended, based on the results to date.


2.5.1 Vegetation Sampling

We collected 21 plant samples, one from each crop type present in each section of land on the project site, in August 2012 (Figure 9). Sampling was stratified by crop type because natural lands and ruderal habitats are no longer irrigated with project water. The pastures on the project site contain native and nonnative plants, both of which were represented in our samples from pastures. Sections of land that overlapped the project site by less than 25% were exempted unless there was a unique crop present. Plant samples included vegetative structures (leaves and stalks) and, if present, fruiting parts (flowers, seeds, or fruits), which were collected when plants were green and showing no signs of water stress. The samples were placed in labeled plastic bags and stored on ice for return to the H. T. Harvey & Associates laboratory. The samples were cleaned, dried, placed into Whirl-Pak sterile sample bags, and frozen before shipment to an analytical facility. All plant samples were shipped overnight on dry ice to South Dakota Agricultural Laboratories. The samples were homogenized and analyzed for selenium content. The results included selenium content by wet weight, sample percent moisture, sample dry weight, selenium content by dry weight, and sample detection limit. A report of duplicates, spikes, and reference samples was provided for quality control. Selenium results were reported on a dry-weight basis.

2.5.2 Small Mammal Sampling

Small mammal sampling was similar in design to the vegetation sampling; one mouse was trapped in each crop type within each section of the project site, for a total of 21 sample locations (Figure 9). At each sample location, we established grids consisting of either 4 rows of 5 stations or 2 rows of 10 stations, spaced 10 meters apart. At each station, a single Sherman LFA live trap was placed on the ground and baited with a mixture of millet and sunflower seeds. From 6 August through 27 September 2012, traps were set during the day and checked for captured animals each morning. Captured mice were euthanized by cardiopulmonary compression, individually bagged, labeled, and placed on ice for shipment to the laboratory. In H. T. Harvey & Associates’ laboratory, collected mice were cleaned and measured for total weight, total length, tail length, and ear length. We also noted the age (juvenile, adult) of each captured individual based on pelage characteristics. Whole mice samples were shipped overnight on dry ice to South Dakota Agricultural Laboratories. The samples were homogenized and analyzed for selenium content using the Association of Official Analytical Chemists method 996.16. The results included selenium content by wet weight, sample percent moisture, sample dry weight, selenium content by dry weight, and sample detection limit. A report of duplicates, spikes, and reference samples was provided for quality control. Selenium results were reported on a dry-weight basis.

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Copyright:© 2013 Esri, DeLorme, NAVTEQ, TomTom, Source: Esri, DigitalGlobe, GeoEye, i-cubed,USDA, USGS, AEX, Getmapping, Aerogrid, IGN, IGP, swisstopo, and the GIS User Community

LEGENDLocations of Reference VegetationSamples and Small Mammals TrappedLocations of Project Site VegetationSamples and Small Mammals TrappedEastern ProjectWestern Project

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Figure 9: Locations of Vegetation Samples Collected and Small Mammals Trapped in 2012October 2013

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2.5.3 Plant and Small Mammal Chemistry Analysis

Plant and small mammal samples collected from the western project area were considered reference samples from 2008 through 2011. In 2012, however, at least some drainwater was applied to fields in Sections 1, 31, 32, and 36 in the western project area. These fields received varying combinations of drainwater and standard irrigation water. Drainwater has not yet been applied to Sections 4, 5, and 6 in the western project area. Since the sample sizes of the 2 different water treatments of the western project area are so small, 4 for partial drainwater and 2 for no drainwater, statistical analysis were not performed between the three types of water treatments on the eastern and western project areas.


Section 3.0 Results

3.1 Bird Censuses

In the eastern project area, 39 avian species were observed between 30 April and 18 June 2012 (Table 1). Avian numbers were highest in late April, when the number of resident birds was augmented by spring migrants (Table 1). Sixteen species were either observed nesting or were suspected of nesting, based on observations of courtship behavior or young. Total bird numbers declined as the season progressed and migrants passed through, as black-necked stilts and American avocets were hazed from the eastern project area, and as project site farming activities intensified. The only exception to the downward seasonal trend occurred on 18 June 2012, when a post-nesting flock of 260 tree swallows (Tachycineta bicolor) congregated on utility wires in the eastern project area. The avian species composition observed in the western project area was similar to that reported for the eastern project area, with a few notable differences (Table 2). For instance, black phoebes (Sayornis nigricans) and marsh wrens (Cistothorus palustris) were absent from the eastern project area, but were present in small narrow strips of marsh and riparian habitat situated parallel to ditches in, and on the periphery of, the western project area. Black-necked stilts and American avocets were absent from the western project area.

3.2 Egg Collection and Processing

Eighteen eggs, comprising 7 killdeer eggs and 11 red-winged blackbird eggs, were collected from the eastern project area. No recurvirostrid nests were found in the eastern project area in 2012. Two killdeer embryos were 15 days old, and were alive and in normal condition. The remaining 5 killdeer embryos were too young (fewer than 9 days old) for their condition to be assessed, although 2 embryos were old enough (more than 3 days old) for us to determine that they were alive at the time of collection (Table 3). Two red-winged blackbird eggs contained live, normal embryos at least 11 days old. The 9 remaining red-winged blackbird embryos were too young (approximately 6 days old) for the statuses of the embryos to be determined, although 5 were old enough for us to determine that they were alive (Table 4). Thirty-one eggs (10 killdeer, 10 recurvirostrids, and 11 red-winged blackbirds) were collected from the reference area. Four killdeer embryos from the reference area were 13 days old or older, alive, and in normal condition. The remaining 6 killdeer embryos were too young to determine the embryo status, although all were old enough for us to determine that they were alive (Table 5). Two of the reference area recurvirostrid eggs contained live, normal embryos 9 days old or older. The 8 remaining recurvirostrid embryos were too young (fewer than 9 days old) for the statuses of the embryos to be determined, although 3 were old enough (3 days old or older) for us to determine that they were alive (Table 6). One red-winged blackbird embryo from the reference area was 10 days old, alive, and in normal condition. Nine red-winged blackbird embryos were too young for their statuses to be determined, although one was old enough for us to


Table 1. Avian Census Results in the Eastern Project Area—San Joaquin River Water Quality Improvement Project

Species 2012

April 30 May 8 May 21 May 28 June 4 June 18 Gadwall 9 Mallard 12 7 13 3 8 Great blue heron 1 3 2 1 Great egret 2 2 1 1 Snowy egret 1 4 2 Cattle egret 19 7 White-faced ibis 31 11 Northern harrier 2 2 2 1 2 1 * Swainson's hawk 4 4 3 4 4 5 Red-tailed hawk 3 3 1 1 1 American kestrel 1 2 1 2 2 2 * Killdeer 16 14 17 16 21 * Black-necked stilt 28 22 American avocet 34 30 Whimbrel 58 49 13 Spotted sandpiper 1 2 Black tern 1 2 1 * Mourning dove 21 11 18 22 * Barn owl 2 4 4 4 2 2 * Burrowing owl 2 2 3 5 4 3 Western wood-pewee 1 2 * Western kingbird 21 19 20 18 22 24 * Loggerhead shrike 2 1 3 2 1 1 Common raven 14 3 6 11 2 7 * Horned lark 12 9 7 8 3 5 Tree swallow 260 Northern rough-winged swallow 4 6 2 * Barn swallow 24 23 24 31 39 49 Cliff swallow 21 51 32 4 * Song sparrow 3 1 Savannah sparrow 21 15 3 Western tanager 1 3 1 * Red-winged blackbird 261 280 254 243 185 145 * Western meadowlark 15 17 19 16 13 9 * Brewer's blackbird 26 25 25 28 32 36 * Brown-headed cowbird 7 6 4 2 1 Bullock's oriole 3 2 2 1 * House finch 41 39 44 47 43 49 * House sparrow 29 30 36 32 31 41 Total 743 705 576 502 421 641 Observed density (birds/acre) 0.186 0.176 0.144 0.126 0.105 0.160

*Species for which evidence of nesting was observed this year.


Table 2. Avian Census Results in the Western Project Area—San Joaquin River Water Quality

Improvement Project

Species 2012

April 30 May 8 May 21 May 28 June 4 June 18 Mallard 8 2 4 4 5 6 Great blue heron 6 2 7 1 Great egret 4 3 7 2 Snowy egret 1 3 3 2 Cattle egret 26 Black-crowned night heron 2 6 11 White-faced ibis 25 17 210 Northern harrier 1 2 1 1 1 1 * Swainson's hawk 3 2 56 1 2 2 * Red-tailed hawk 2 4 3 2 1 American kestrel 1 1 1 2 1 * Killdeer 8 11 10 12 11 10 Long-billed curlew 62 * Mourning dove 6 12 14 9 7 4 Barn owl 1 2 * Great horned owl 3 2 3 1 1 1 * Black phoebe 5 4 5 4 2 3 Western wood-pewee 1 4 1 * Western kingbird 14 18 21 22 20 23 * Loggerhead shrike 5 6 4 5 5 3 Common raven 2 1 24 1 3 * Horned lark 6 5 4 6 4 2 Tree swallow 21 7 136 Northern rough-winged swallow 4 6 2 * Barn swallow 9 10 12 10 14 20 Cliff swallow 21 17 8 4 House wren 1 2 1 1 1 1 * Marsh wren 1 2 1 1 1 Northern mockingbird 1 2 1 2 2 2 Savannah sparrow 6 8 * Song sparrow 4 6 3 4 2 3 Black-headed grosbeak 1 3 1 * Blue grosbeak 1 2 1 1 2 1 * Red-winged blackbird 156 162 155 149 127 130 Tricolored blackbird 72 124 * Western meadowlark 21 22 18 22 21 17 * Brewer's blackbird 24 28 31 34 21 11 * Brown-headed cowbird 11 8 9 5 2 * Bullock's oriole 4 6 5 6 8 8 * House finch 31 28 26 41 29 21 * House sparrow 17 22 24 20 16 11 Total 508 443 902 372 308 424 Observed density (birds/acre) 0.267 0.233 0.474 0.196 0.162 0.223

*Species for which evidence of nesting was observed this year.


determine that it was alive. The remaining embryo was undeveloped, likely as a result of being abandoned (Table 7). Three black-necked stilt and 2 American avocet eggs were collected from the mitigation site. Two of these eggs contained live, normal embryos 17 days old or older. The 3 remaining embryos were too young (fewer than 9 days old) for their embryo status to be determined, although 2 were old enough (3 days old or older) for us to determine that they were alive (Table 8).

Table 3. Eastern Project Area Killdeer Egg-selenium Concentrations—San Joaquin River Water Quality Improvement Project

ID Number

Field Numbera

Date 2012

Embryo Embryo Age (days)

Selenium (ppm, dry wt)d

Log Base 10

Anti-log Conditionb Statusc

01 PK-02 May 11 U U 1 19.2 1.2833

02 PK-05 June 8 L N 15 17.4 1.2405

03 PK-06 June 14 L N 15 43.0 1.6335

04 PK-07 June 14 L U 3–6 32.7 1.5145

05 PK-08 June 20 U U 1 13.5 1.1303

06 PK-09 June 20 U U 1–3 8.14 0.9106

07 PK-10 June 29 L U 6 26.2 1.4183

Arith./Geo. Mean 22.9 1.3044 20.2

Standard Deviation 12.0 0.2433 1.8

Standard Error 0.1088 1.3

Lower limit of 95% confidence interval 1.0911 12.3

Upper limit of 95% confidence interval 1.5177 32.9 Notes: a See Appendix K. b L = live, D = dead, U = unknown. c N = normal, A = abnormal, U = unknown. d ppm, dry wt = parts per million dry weight.


Table 4. Eastern Project Area Red-winged Blackbird Egg-selenium Concentrations—San Joaquin River Water Quality Improvement Project

ID Number

Date 2012


Selenium (ppm, dry wt)c

Log Base 10

Anti-log Conditiona Statusb

01 May 4 U U 1 12.8 1.1072

02 May 7 L U 7 9.00 0.9542

03 May 11 L U 2 9.10 0.9590

04 May 22 L N 11 10.0 1.0000

05 May 22 L N 11 10.5 1.0212

06 May 22 U U 1 10.5 1.0212

07 May 22 L U 5 5.62 0.7497

08 May 22 U U 1 6.83 0.8344

09 May 22 U U 1 5.90 0.7709

10 May 22 L U 4 8.56 0.9325

11 May 22 L U 4 5.71 0.7566

Arith./Geo. Mean 9.1 0.9518 9.0




Upper limit of 95% confidence interval 1.0189 10.4 Notes: a L = live, D = dead, U = unknown. b N = normal, A = abnormal, U = unknown. c ppm, dry wt = parts per million dry weight.


Table 5. Reference Area Killdeer Egg-selenium Concentrations—San Joaquin River Water Quality Improvement Project

ID Number

Date 2012



Log Base 10


01 May 11 L U 3 24.9 1.3962

02 May 15 L U 8 2.27 0.3560

03 May 15 L U 8 3.28 0.5159

04 May 15 L U 6 4.28 0.6314

05 May 18 L N 17 9.32 0.9694

06 June 1 L U 6–9 5.68 0.7543

07 June 1 L N 14 11.2 1.0492

08 June 1 L N 15 5.31 0.7251

09 June 18 L U 3–6 2.97 0.4728

10 June 27 L N 13 39.3 1.5944

Arith./Geo. Mean 10.85 0.8465 7.0





Table 6. Reference Area Recurvirostrid Egg-selenium Concentrations—San Joaquin River Water Quality Improvement Project

ID Number Species

Date 2012



Log Base 10


01 Black-necked stilt May 4 U U 1 32.0 1.5051

02 Black-necked stilt May 15 L N 9 11.5 1.0607




06 Black-necked stilt June 8 L U 3 13.3 1.1239

07 Black-necked stilt June 8 L U 3–6 5.10 0.7076

08 Black-necked stilt June 14 U U 1 13.5 1.1303

09 Black-necked stilt June 14 L U 3–6 12.6 1.1004

10 Black-necked stilt June 18 L N 14 20.3 1.3075

Arith./Geo. Mean 13.2 1.0391 10.9






Table 7. Reference Area Red-winged Blackbird Egg-selenium Concentrations—San Joaquin River Water Quality Improvement Project

ID Number

Date 2012


Selenium (ppm, dry

wt)c

Log Base 10


01 May 29 U U 1 5.38 0.7308

02 May 29 U U 1 4.15 0.6180

03 May 29 U U 1 5.11 0.7084

04 May 29 U U 1 4.25 0.6284

05 May 29 U U Undevelopedd 3.21 0.5065

06 May 29 U U 1 4.56 0.6590

07 May 29 L N 10 4.72 0.6739

08 May 29 L U 3 4.65 0.6675

09 May 29 U U 1 3.75 0.5740

10 May 29 U U 1 4.04 0.6064

11 May 29 L U 2 3.68 0.5658

Arith./Geo. Mean 4.3 0.6308 4.3




Upper limit of 95% confidence interval 0.6887 4.9 Notes: a L = live, D = dead, U = unknown. b N = normal, A = abnormal, U = unknown. c ppm, dry wt = parts per million dry weight. d Undeveloped, likely due to abandonment.


Table 8. Mitigation Site Recurvirostrid Egg-selenium Concentrations—San Joaquin River Water Quality Improvement Project

ID Number

Field Numbera

Date 2012



Log Base 10


Black-necked stilt

01 PM S-04 June 1 U U 1 4.78 0.6794

02 PM A-08 June 4 L N 20+ 7.34 0.8657

03 PM A-09 June 4 L N 17 6.10 0.7853

04 PM A-10 June 4 L U 3–6 4.26 0.6294

05 PM A-11 June 4 L U 3 5.12 0.7093

Arith./Geo. Mean 5.5 0.7338 5.4




Upper limit of 95% confidence interval 0.8152 6.5 Notes: a See Appendix K. b L = live, D = dead, U = unknown. c N = normal, A = abnormal, U = unknown. d ppm, dry wt = parts per million dry weight.


3.3 Egg-Selenium Analysis

3.3.1 2012 Egg-Selenium Data Analysis between Sites

In 2012, egg-selenium concentrations varied considerably between locations and species. Egg-selenium concentrations were significantly higher in eggs collected from the eastern project area than from eggs collected from the reference area for killdeer and red-winged blackbirds (Table 9). There were no recurvirostrids in the eastern project area in 2012. Table 9. 2012 Geometric Mean Egg-selenium Concentrations—San Joaquin River Water Quality

Improvement Project

Location n Geo. Mean

(ppm Se, dry wt)a Range

Killdeer

Eastern project area 7 20.2 8.14–43.0

Offsite reference sample 10 7.0

2.27–39.3

Significant difference (F1,15 = 6.919, P = 0.0189) between sites

Recurvirostrids

Eastern project area 0 n/a n/a

Offsite reference sample 10 10.9 3.47–32.0

Difference between sites: n/a

Red-winged blackbirds



Significant difference (F1,20 = 110.800, P < 0.0001) between sites Notes: a ppm se, dry wt = parts per million selenium dry weight.

3.3.2 Egg-selenium Data Analysis across Years

For killdeer, a gamma GLM was used to evaluate the effects of location and year. Initially, evaluation of the simple linear regression model residuals showed indications of heterogeneity (particularly between sites) and led to fitting of a weighted regression model. Examination of residuals from the weighted regression indicated a non-normal distribution of normalized residuals, prompting use of a model with a different error distribution. We chose the GLM because it allows for a skewed error distribution (as suggested by the distribution of normalized residuals [results not shown]). When comparing the full models (i.e., with location, year, and interaction terms), the gamma GLM had a substantially lower AIC score (-109.1), indicating better model fit, compared to the weighted regression model (-90.1) and the original linear model (-81.0). An


examination of residuals (see Appendix A, Figure A1) showed that the assumptions regarding homogeneity and independence were met with the final model. Killdeer egg-selenium concentrations were consistently greater in the eastern project area than in the reference area (Figure 10), and this was confirmed by analyses (Table 10, Figure 11). There was a significant effect due to location and year (cubic); but the interaction between location and year was inconclusive, indicating that the relationship between egg-selenium concentrations and year may differ between the project site and reference area (Figure 11).

Figure 10. Mean ± 95% Confidence Interval Egg-selenium Concentrations for Killdeer at the San

Joaquin River Water Quality Improvement Project (2002 to 2012) Table 10 shows the results of GLMs or linear regression models regarding the effects of location and year on selenium concentrations in killdeer eggs at the SJRIP from 2002 to 2012, and in recurvirostrid, and red-winged blackbird eggs at the SJRIP from 2003 to 2012. Interaction is the location x yearn interaction effect, and year is either a second-order (quadratic) or third-order (cubic) polynomial. The test statistic is X2 for GLMs and F for linear models.


Table 10. Effects of Location and Year on Egg-selenium Concentrations in Killdeer (2002 to

2012), and Recurvirostrids and Red-winged Blackbirds (2003 to 2012)—San Joaquin River Water Quality Improvement Project

Avian Species Group Element Term Χ2 or (F) Dfa P

Killdeer (GLM) Selenium Location 184.7800 1 <0.0001

Year (quadratic) 4.8742 3 0.0387

Interaction 3.0063 3 0.0810

Recurvirostrids (linear model)

Selenium Location (63.9317) 1 <0.0001

Year (quadratic) (5.3398) 2 0.0115

Interaction (0.4630) 2 0.4414

Red-winged blackbirds (GLM)

Selenium Location 159.0100 1 <0.0001

Year (cubic) 7.6586 3 0.0011

Interaction 16.9000 3 0.0015 Notes: a Df = degrees of freedom. For recurvirostrids, a simple linear regression model was used because model assumptions regarding homoscedasticity, normality, and independence were all met (see Appendix A, Figure A2). Recurvirostrid egg-selenium concentrations were typically greater in the eastern project area than in the reference area (Figure 12), and analyses also showed a significant location effect. In addition, analyses indicated a significant relationship with year (quadratic) (Table 10, Figure 13). However, the interaction between location and year was not significant, indicating that the relationship between concentration and year did not differ between project site and reference area. For red-winged blackbirds, we decided to use a GLM with a gamma error distribution. This model accounts for a non-normal error, which was indicated by inspection of the residuals; there was no clear pattern in the residuals that would suggest either heteroscedasticity or lack of independence. The gamma GLM had a substantially lower AIC score (-426.8, full model) than the simple linear model (-391.3, full model), indicating better model fit as well. Examination of residuals for the final model (see Appendix A, Figure A3) showed that the assumptions regarding homogeneity and independence were met with the final model. Red-winged blackbird egg-selenium concentrations appeared to be typically greater in the eastern project area than in the reference area (Figure 14), and analyses showed a significant location and year effect (Table 10). The test result for the interaction was also significant (Table 10), indicating that the relationship with year (cubic) differs between the 2 areas (Figure 15).


Figure 11. Predicted Egg-selenium Concentrations with 95% Confidence Bands for Killdeer at the

San Joaquin River Water Quality Improvement Project (2002 to 2012)


Figure 12. Mean ± 95% Confidence Interval Egg-selenium Concentrations for Recurvirostrids at

the San Joaquin River Water Quality Improvement Project (2003 to 2012)


Figure 13. Predicted Egg-selenium Concentrations with 95% Confidence Bands for Recurvirostrids

at the San Joaquin River Water Quality Improvement Project (2003 to 2012)


Figure 14. Mean ± 95% Confidence Interval Egg-selenium Concentrations for Red-winged

Blackbirds at the San Joaquin River Water Quality Improvement Project (2003 to 2012)


Figure 15. Predicted Egg-selenium Concentrations with 95% Confidence Bands for Red-winged



3.3.3 Recurvirostrid Mitigation Site Selenium Concentrations

As in 2011, 2012 selenium concentrations in recurvirostrid eggs differed significantly among sites based on one-way ANOVA (F1,13 = 5.102, P = 0.0417, Figure 16), in contrast to the results of 2009 and 2010 (H. T. Harvey & Associates 2010, 2011). Because there were no recurvirostrid nests on the project site in 2012, the test result indicates a difference between the reference area and mitigation site only; in contrast to this result, no difference was found between the reference area and mitigation site in 2011. The 2012 results should be viewed with some caution, however, because relatively few nests were sampled at the mitigation site (n = 5).

Reference Mitigation

0.5

0.7

0.9

1.1

1.3

Log 1

0(E

gg-S

elen

ium

con

c.+1

)

Figure 16. Mean ± 95% Confidence Interval Egg-selenium Concentrations for Recurvirostrids at

the San Joaquin River Water Quality Improvement Project (2012)


3.4 Egg-boron Analysis

3.4.1 2012 Egg-boron Data Analysis between Sites

As in 2011, there were statistical differences between the boron concentrations of killdeer and red-winged blackbird eggs collected from the eastern project area and those of eggs collected from the reference area in 2012 (Table 11). Because no recurvirostrid eggs were sampled in the eastern project area, no test was conducted for recurvirostrids. Three eggs collected in 2012 had boron levels that were below the detection limit of the method used. A value on one half the detection limit (0.07 ppm) was substituted for zero in these instances, for all analyses. Raw boron data are presented in Appendices B, C, and D. Table 11. 2012 Geometric Mean Egg-boron Concentrations—San Joaquin River Water Quality

Improvement Project

Location n Geo. Mean (ppm B, dry wt)a Range

Killdeer




Recurvirostrids







Significant difference (F1,20 = 51.470, P < 0.0001) between sites Notes: a ppm se, dry wt = parts per million boron dry weight.

3.4.2 Egg-boron Data Analysis across Years

For killdeer, we used a linear regression model that incorporated a temporal correlation structure. Initially, inspection of the residuals indicated that there was a lack of independence. The revised model with temporal correlation structure was substantially better (~SITE+YEAR^2, AIC = -147.5, full model) compared to the original linear model (AIC = -121.6). In addition, the residuals were better behaved overall (homoscedastic and no pattern) in the model with a temporal correlation structure (see Appendix A, Figure A4).


As in previous years, in 2012, killdeer egg-boron concentrations were significantly greater in the eastern project area than in the reference area (Table 11, Figure 17). The multiyear analysis indicated a significant location effect, a significant quadratic relationship with year, and no interaction between location and year (Table 12, Figure 18).

Figure 17. Mean ± 95% Confidence Interval Egg-boron Concentrations for Killdeer at the San

Joaquin River Water Quality Improvement Project (2002 to 2012) The results of linear regression models regarding the effects of location and year on boron in killdeer eggs at the SJRIP from 2002 to 2012, and in recurvirostrid, and red-winged blackbird eggs at the SJRIP from 2003 to 2012 are shown in Table 12. Linear regression models included specified residual temporal correlation structure (killdeer, red-winged blackbirds) and/or variance structure (killdeer). Interaction is the location x yearn interaction effect, and year is a linear term, or a second-order (quadratic) or third-order (cubic) polynomial.


Table 12. Effects of Location and Year on Egg-boron Concentrations in Killdeer, Recurvirostrids, and Red-winged Blackbirds (2003 to 2012)—San Joaquin River Water Quality Improvement Project

Avian Species Group Element Term Χ2 Dfa P

Killdeer (Linear model)

Boron Location 23.5618 1 <0.0001



Recurvirostrids (GLM) Boron Location 1.9606 1 0.1615



Red-winged blackbird (Linear model)

Boron Location 27.8390 1 <0.0001


Interaction 29.5890 2 <0.0001 Notes: a Df = degrees of freedom.


Figure 18. Predicted Egg-boron Concentrations with 95% Confidence Bands for Killdeer at the


For recurvirostrids, we used a GLM to evaluate the effects of location and year. Examination of residuals from the initial linear regression model fit indicated a non-normal distribution of residuals, prompting use of a model with a different error distribution. We chose the gamma GLM, because it allows for a skewed error distribution (as suggested by the distribution of normalized residuals [results not shown]). When comparing the full models (i.e., with location, year, and interaction terms), the gamma GLM model had a substantially lower AIC score (48.3), indicating better model fit, compared to the original linear model (54.6). An examination of residuals (see Appendix A, Figure A5) showed that the assumptions regarding homogeneity and independence were met with the final model. Across years, recurvirostrid egg-boron concentrations fluctuated considerably in both the eastern project area and the reference area (Figure 19), and analyses suggested that there was a significant relationship with time


(quadratic year term) (Table 12), with a largely decreasing trend over the past 5 years (Figure 20). Neither the location effect nor the interaction between location and year were significant (Table 12).

Figure 19. Mean ± 95% Confidence Interval Egg-boron Concentrations for Recurvirostrids at the



Log 1

0(E

gg-B

oron

con

c.+1

)

Year

2003 2005 2007 2009 2011

0.0

0.2

0.4

0.6

0.8

1.0

1.2

Figure 20. Predicted Egg-boron Concentrations with 95% Confidence Bands for Recurvirostrids at

the San Joaquin River Water Quality Improvement Project (2003 to 2012) (Note that Location Was Not a Significant Effect in the Model)

For red-winged blackbirds, we used a model that incorporated temporal correlation structure. The initial evaluation of the residuals revealed a pattern of increasing spread with year, leading to further evaluation of autocorrelation. The autocorrelation plot revealed that several time lags had significant correlation, showing that the assumption of independence was violated. Once we incorporated a temporal correlation structure, we arrived at a model that better met the assumptions (see Appendix A, Figure A6), and fit the data much better (AIC score of -111.4 compared to -70.4, a dramatic improvement).


Red-winged blackbird egg-boron concentrations appeared to be typically greater in the eastern project area than in the reference area, although patterns were variable (Figure 21). The main effect for location was significant (Table 12). Although the main effect for year (quadratic term) was not significant, the relationship between egg-boron concentration and year did differ significantly by location, as indicated by a significant interaction between location and year (Table 12). There appeared to be little change with time for the eastern project area, whereas there appeared to be a decreasing trend with time for the reference area (Figure 22).

Figure 21. Mean ± 95% Confidence Interval Egg-boron Concentrations for Red-winged



Figure 22. Predicted Egg-boron Concentrations with 95% Confidence Bands for Red-winged



3.4.3 Recurvirostrid Mitigation Site Boron Concentrations

In 2012, boron concentrations in recurvirostrid eggs did not differ among sites based on one-way ANOVA (F1,13 = 0.246, P = 0.628), similar to 2010 (H. T. Harvey & Associates 2011) and 2011 (H. T. Harvey & Associates 2012). The 95% confidence intervals in 2012 were relatively wide for both the reference area and the mitigation site (Figure 23), although this may be due to natural variation, at least for the reference area, because the sample size was reasonable (n = 10 for reference area). However, the sample size for the mitigation site was relatively small (n = 5), so results should be viewed with consideration of that caveat.


-0.4

-0.2

00.

20.

40.

60.

81

1.2

Log 1

0(E

gg-B

oron

con

c.+1

)

Figure 23. Mean ± 95% Confidence Interval Egg-boron Concentrations for Recurvirostrids at the

San Joaquin River Water Quality Improvement Project (2012)


3.5 Egg-mercury Analysis

3.5.1 2012 Egg-mercury Data Analysis between Sites

Comparison of egg-mercury concentrations between locations, based on one-way ANOVA of 2012 data, showed a significant difference between sites for killdeer and red-winged blackbirds (Table 13). No recurvirostrids were found in the eastern project area, so no comparison was possible for them. Raw mercury data are presented in Appendices E, F, and G. Table 13. 2012 Geometric Mean Egg-mercury Concentrations—San Joaquin River Water Quality

Improvement Project

Location n Geo. Mean (ppm Hg, wet wt)a Range

Killdeer




Recurvirostrids







Significant difference (F1,20 = 5.104, P = 0.0352) between sites Notes: a ppm Hg wet wt = parts per million mercury wet weight.

3.5.2 Recurvirostrid Mitigation Site Mercury Concentrations

In 2012, mercury concentrations in recurvirostrid eggs did not differ significantly between the reference area and the mitigation site based on one-way ANOVA (F1, 13 = 0.269, P = 0.613), although the 95% confidence intervals in 2012 were relatively large for the mitigation site in particular (Figure 24). Because there were relatively few eggs collected (n = 5) from the mitigation site, the power of the test is low.



00.

020.

040.

060.

080.

10.

120.

140.

16

Log 1

0(E

gg-M

ercu

ry c

onc.

+1)

Figure 24. Mean ± 95% Confidence Interval Egg-mercury Concentrations for Recurvirostrids at

the San Joaquin River Water Quality Improvement Project (2012)

3.6 Control Eggs

An average value of 2.00 milligrams per kilogram (mg/kg) selenium was obtained using National Institute of Standards (NIST) Standard Reference Material 1577c (certified value = 2.03 ± 0.145 micrograms per gram [µg/g]). The standard deviation of selenium results from 6 duplicate control egg samples ranged between 0.0778 and 3.1113, with a mean standard deviation of 1.0147 (Appendix H). The boron recovery rate for 4 egg samples spiked with boron ranged between 101% and 105%, with a mean boron recovery rate of 102.5% (Appendix I). The standard deviation of boron results from 12 duplicate control egg samples ranged between 0.0071 and 0.1909, and the mean standard deviation was 0.0601 (Appendix I). The standard deviation of mercury results from 7 duplicate control egg samples ranged between 0.212 and 21.213, and the mean standard deviation was 6.839 (Appendix J).


3.7 Nest Fate

Ten killdeer nests in the eastern project area were followed to completion in 2012 (Table 14, Appendix K). Three of the killdeer nests hatched, 3 were lost to predators, and 4 were inadvertently destroyed by farming activities. No black-necked stilt or American avocet nests were present in the eastern project area in 2012 (Appendix K). Three killdeer nests and 19 recurvirostrid nests were monitored at the mitigation site. All 3 of the killdeer nests and 9 of the recurvirostrid nests hatched successfully. Predators took the remaining 10 recurvirostrid nests (Table 14, Appendix K). Table 14. Nest Fates and Agents that Caused Nest/Clutch Success or Failure in the Eastern

Project Area and Mitigation Site in 2012—San Joaquin River Water Quality Improvement Project

Species

Hatched Depredated Levee

Maintenance Activities

Vehicle/ Farm Activities

Total Nests % Nests % Nests % Nests %

Eastern project area

Killdeer 3 30 3 30 4 40 10

Recurvirostrids 0

Black-necked stilt (0)

American avocet (0)

Total 3 30 3 30 4 40 10

Mitigation site

Killdeer 3 100 3

Recurvirostrids 9 47 10 53 19

Black-necked stilt (3) (3) (6)

American avocet (6) (7) (13)

Total 12 55 10 45 22

3.8 Mitigation Site Water Quality

The results of the water quality analysis for the mitigation site are summarized in Table 15. Selenium and boron concentrations in the water sample from the mitigation site inlet were well below the 2.3 ppb selenium


and 5 ppm boron thresholds for wildlife safety in freshwater (Eisler 1990; Skorupa and Ohlendorf 1991; Suter 1996). Outlet water selenium was also below the threshold, but boron slightly exceeded the threshold. Table 15. Water Quality in Samples Taken from the Mitigation Site on 2 June 2012—San Joaquin

River Water Quality Improvement Project

Electrical Conductivity

(µhmo/cm)a Boron (ppm)

Selenium (ppb)

Freshwater thresholdsb 5 2.3

Location

Inlet 499 0.288 <1

Middle 993 1.21 <1

Outlet 2520 5.71 2.0

Notes: a µhmo/cm = micromhos per centimeter. b From Eisler 1988, 1989, 1990; Skorupa and Ohlendorf 1991; Suter 1996.

3.9 Tiered Biological Monitoring Program

3.9.1 Vegetation Sampling and Selenium Analysis

Twenty-one vegetation samples were analyzed for selenium (Table 16): 15 samples from 5 crop types in the eastern project area and 6 samples from 3 crop types in the western project area, which was used as the reference area for the plant and mammal selenium analyses. The eastern project area sample crop types were Jose tall wheatgrass, pasture, pasture/Bermuda, pasture/paspallum, and alfalfa. The crop types sampled from the western project area were Jose tall wheatgrass, alfalfa, and row crop. Eight plant samples exceeded the 3 ppm threshold of concern for the dietary effects of plant-selenium on mammals, established in the BO (Table 16). All of the 8 samples were from the eastern project area; 5 were Jose tall wheatgrass, 2 were pasture, and one was pasture/paspallum. Salt tolerant crops were utilized on the western project area this year. Crops in sections 1, 31, 32, and 36 received at least some drain water during the year, but unlike the eastern project area where crops are irrigated exclusively with drainwater, a mix of standard irrigation water and drainwater was applied in 2012. Crops in sections 4, 5, and 6 did not receive drainwater in 2012 (Table 16). Selenium levels appeared to vary quite a bit between species in the eastern project area: the concentrations of selenium in Jose tall wheatgrass, pasture, and pasture/paspallum were substantially higher than in alfalfa and pasture/Bermuda. However, in the western project area, it appeared that alfalfa, Jose tall wheatgrass, and row crops had similar mean selenium concentrations (Table 17).


Table 16. Project Site Plant-selenium Concentrations—San Joaquin River Water Quality Improvement Project

ID Number Crop Date

2012 Sample Location

Selenium (ppm, dry wt)a

Log Base 10 Anti-log

Eastern project area 01 Pasture Sept. 19 Field 2-4 4.27 0.6304

02 Jose tall wheatgrass Sept. 13 Field 2-8 2.29 0.3598 03 Pasture/Bermuda Sept. 20 Field 3-5 1.61 0.2068

04 Jose tall wheatgrass Aug. 24 Field 3-6 4.69 0.6712 05 Jose tall wheatgrass Sept. 6 Field 10-7 4.55 0.6580

06 Jose tall wheatgrass Aug. 7 Field 11-2 2.64 0.4216

07 Pasture/paspallum Sept. 5 Field 12-1 3.27 0.5145 08 Jose tall wheatgrass Aug. 14 Field 12-3 6.45 0.8096

09 Jose tall wheatgrass Aug. 14 Field 13-2 2.37 0.3747 10 Alfalfa Aug. 22 Field 13-6 2.89 0.4609


12 Pasture Aug. 16 Field 14-4 3.50 0.5441 13 Alfalfa Aug. 16 Field 15-2 1.13 0.0531


15 Jose tall wheatgrass Aug. 17 Field 18-2 4.80 0.6812 Arith./Geo. Mean 3.479 0.5021 3.18 Standard Deviation 1.433 0.2011 1.59 Standard Error 0.0899 1.23 Lower limit of 95% confidence interval 0.3258 2.12 Upper limit of 95% confidence interval 0.6783 4.77

Western project area Western project area fields where some drainwater was applied

01 Jose tall wheatgrass Sept. 21 Field 1-1 1.82 0.2601 02 Jose tall wheatgrass Sept. 25 Field 31-2 2.59 0.4133

03 Jose tall wheatgrass Oct. 2 Field 32-2 1.24 0.0934 04 Jose tall wheatgrass Oct. 5 Field 36-2 1.26 0.1004

Arith./Geo. Mean 1.728 0.2168 1.65 Standard Deviation 0.635 0.1519 1.42 Standard Error 0.0680 1.17 Lower limit of 95% confidence interval 0.0836 1.21 Upper limit of 95% confidence interval 0.3500 2.24


ID

Number Crop Date 2012

Sample Location

Selenium (ppm, dry wt)a


Western project area fields where drainwater had not yet been applied 01 Row crop Sept. 27 Field 4-3 0.416 -0.3809 02 Alfalfa Oct. 5 Field 5-4 0.957 -0.0191

Arith./Geo. Mean 0.687 -0.2000 0.63 Standard Deviation 0.383 0.2558 1.80 Standard Error 0.1144 1.30 Lower limit of 95% confidence interval -0.4243 0.38 Upper limit of 95% confidence interval 0.0243 1.06

Notes: a ppm, dry wt = parts per million dry weight.

.

Table 17. 2012 Vegetation Selenium Concentrations by Crop Type and Location—San Joaquin River Water Quality Improvement Project

Crop

Eastern Project Area Western Project Area

n Geo. Mean

(ppm Se, dry wt)a n

Geo. Mean (ppm Se, dry wt)a

Alfalfa 2 1.81 1 0.96

Jose tall wheatgrass 9 3.71 4 1.65

Pasture 2 3.87

Pasture/Bermuda 1 1.61

Pasture/paspallum 1 3.27

Row crop 1 0.42 Notes: a ppm Se, dry wt = parts per million Selenium, dry weight.

3.9.2 Small Mammal Sampling and Selenium Analysis

In 2012, 18 deer mice (Peromyscus maniculatus) and 3 house mice (Mus musculus) were captured at 21 sample locations (15 captures in the eastern project area and 6 in the western project area). Nine of these mice samples, 7 from the eastern project area and 2 from the western project area, exceeded the 3 ppm threshold of concern for the dietary effects of selenium on mammals, established in the BO (Table 18). All of the mice captured were adults, except for a juvenile deer mouse caught in Field 12-1 (Table 18).


Table 18. Small Mammal–Selenium Concentrations—San Joaquin River Water Quality Improvement Project

ID Number Species Date

2012 Sample Location Sex Selenium

(ppm, dry wt) Log

Base 10 Anti-log

Eastern project area 01 Deer mouse Sept. 19 Field 2-4 M 1.68 0.2253 02 Deer mouse Sept. 13 Field 2-8 M 5.57 0.7459

03 Deer mouse Sept. 20 Field 3-5 M 1.53 0.1847

04 House mouse Aug. 24 Field 3-6 F 1.32 0.1206 05 House mouse Sept. 6 Field 10-7 M 2.73 0.4362

06 Deer mouse Aug. 7 Field 11-2 M 3.80 0.5798 07 Deer mouse Sept. 5 Field 12-1 Juvenile 1.67 0.2227

08 House mouse Aug. 14 Field 12-3 M 6.35 0.8028

09 Deer mouse Aug. 14 Field 13-2 F 4.88 0.6884 10 Deer mouse Aug. 22 Field 13-6 M 2.77 0.4425

11 Deer mouse Aug. 16 Field 14-1 M 2.44 0.3874

12 Deer mouse Aug. 16 Field 14-4 M 10.1 1.0043 13 Deer mouse Aug. 16 Field 15-2 M 2.46 0.3909

14 Deer mouse Aug. 14 Field 17-2 M 7.09 0.8506 15 Deer mouse Aug. 17 Field 18-2 M 5.02 0.7007

Arith./Geo. Mean 3.96 0.5189 3.30 SD 2.5 0.2718 1.9 SE 0.1215 1.3 Lower limit of 95% confidence interval 0.2807 1.9 Upper limit of 95% confidence interval 0.7571 5.7

Western project area

Western project area mice caught in fields that had received at least some drainwater 01 Deer mouse Aug. 9 1-1 F 5.39 0.7316

02 Deer mouse Aug. 10 31-2 M 2.07 0.3160

03 Deer mouse Aug. 10 32-2 M 1.82 0.2601 04 Deer mouse Aug. 9 36-2 M 3.89 0.5899



ID

Number Species Date 2012

Sample Location Sex Selenium

(ppm, dry wt) Log

Base 10 Anti-log

Western project area mice caught in fields that did not receive any drainwater 02 Deer mouse Aug. 9 4-3 F 1.38 0.1399

03 Deer mouse Aug. 10 5-4 F 1.65 0.2175


Notes: a ppm, dry wt = parts per million dry weight.


Section 4.0 Discussion

In 2012, approximately 5138 acres of the SJRIP site had been planted with salt-tolerant crops and irrigated with agricultural drainwater. Approximately 60 acres of the eastern project area and 758 acres of the western project area were not yet planted with salt-tolerant crops or irrigated with agricultural drainwater. Hazing of birds during the nesting season, diligent water management, and modification of drains to discourage avian use of the project site continued during this reporting period. To date, 7.5 mi of drains have been filled and another 3.4 mi of an open drain have been re-contoured to reduce habitat quality and deter birds from using the site. Hazing and drain closures will continue as part of the operation of the project in future years. The avian census data indicate that the eastern and western project areas are used by bird species common in San Joaquin Valley agricultural habitats. Both avian species diversity and relative abundance were lower in the eastern project area than in the western project area, which, being actively farmed and irrigated with freshwater, more closely characterizes the bird habitat present in the project vicinity. In both areas, the tall vegetation in some pastures provided nesting habitat for red-winged blackbirds, and irrigated pastures and alfalfa fields provided temporary foraging opportunities for birds such as white-faced ibis (Plegadis chihi), long-billed curlew (Numenius americanus), red-winged blackbird, and Brewer’s blackbird (Euphagus cyanocephalus) when wet. Two species listed by the state of California as species of concern, the burrowing owl (Athene cunicularia) and the loggerhead shrike (Lanius ludovicianus), were observed nesting in the eastern project area. The closure of drains in the area has reduced the number of California ground squirrel colonies present, which in turn has reduced the number of burrowing owls inhabiting the eastern project area. Loggerhead shrikes, but not burrowing owls, were also present in the western project area. Swainson’s hawks (Buteo swainsoni), which are listed as threatened by the state of California, were also observed on the project site. One Swainson’s hawk nest was observed in the eastern project area, and an additional nest was situated adjacent to the eastern project area’s border (Figure 2). There were an additional 2 Swainson’s hawk nests in the western project area. The nest on the border of the eastern project area was abandoned after great horned owls (Bubo virginianus) began occupying the nest tree. The remaining 3 Swainson’s hawk nests successfully fledged 2 young each. Hazing of birds during the nesting season, diligent water management, and modification of drains to discourage avian use resulted in fewer killdeer and no recurvirostrid nesting on the project site during this reporting period. Recurvirostrid nests in the eastern project area have decreased from more than 30 in 2003 to just 2 in each year from 2009 to 2011, and to zero in 2012. Killdeer nests had numbered more than 15 per year from 2003, when larger-scale egg sampling began, to 2006, but have been reduced to 11 or fewer since 2007.


Although diligent management has reduced the number of birds exposed to selenium contamination, mean egg-selenium levels in killdeer eggs at the project site in 2012 continued to be above selenium levels associated with a high probability of reproductive effects, including reduced hatchability (CH2MHill et al. 1993). For a more thorough discussion of established egg-selenium thresholds, see the monitoring report for 2005 (H. T. Harvey & Associates 2006). This monitoring period was the fourth to include mercury analysis of eggs. Methylmercury is known to cause embryotoxic effects (Fimreite 1971). Because most of the mercury present in bird eggs has been shown to be methylmercury (Kennamer et al. 2005), sampled eggs were analyzed for whole mercury. Methylmercury embryotoxicity thresholds are not published for the 3 species groups this study samples, and species are known to differ in methylmercury sensitivity (Heinz et al. 2009). Thresholds suggested in Eisler (1987) include less than 0.9 ppm (wet weight) for mallards and pheasants. Based on Fimreite’s 1971 experiment involving mercury dosing of ring-necked pheasants, a lowest observed adverse effect level (LOAEL) of 0.5 ppm (wet weight) egg-mercury concentration is commonly adopted (Service 2003). Project site egg-mercury concentrations ranged from 0.0091 ppm to 0.213 ppm (wet weight). Project site mean egg-mercury concentrations were statistically higher than reference area mean egg-mercury concentrations for both killdeer and red-winged blackbirds. In 2009 and 2010, project site mean egg-mercury concentrations did not statistically differ from reference area mean egg-mercury concentrations for all 3 groups (H. T. Harvey & Associates 2010, 2011). The mitigation site established in 2006 was moved to a new location in 2012. The site was contoured to contain as many islands as possible without having to bring in additional soil, resulting in 7 long contour islands, in addition to the normal check levees. Rice was not planted in the 20-acre portion of the field designated as the mitigation site. The vegetation-free islands constructed in the mitigation site provided improved nesting and foraging habitat for recurvirostrids and killdeer; there were 19 recurvirostrid nest attempts at the mitigation site in 2012. Predation pressure at the mitigation site, mostly from raccoons (Procyon lotor), remained high despite the new location, and likely suppressed the number of recurvirostrids nesting there. Twelve of the 22 shorebird nests located at the mitigation site successfully hatched, whereas 10 of the nests located there were depredated. Eight plant samples exceeded the 3 ppm threshold of concern for dietary effects on mammals, established in the BO. Nine small mammal samples, 7 from the eastern project area and 2 from the western project area, exceeded the 3 ppm threshold of concern for dietary effects on mammals, established in the BO. The samples from the western project area that exceeded the threshold were from fields that had received at least some drainwater.


Section 5.0 Literature Cited

CH2MHill, H. T. Harvey & Associates, and G. L. Horner. 1993. Cumulative Impacts of Agriculture Evaporation Basins on Wildlife. Prepared for California Department of Water Resources.

Eisler, R. 1990. Boron Hazards to Fish, Wildlife, and Invertebrates: A Synoptic Review. Biological report 85

(1.20), Contaminant Hazard Reviews Report No. 20. U.S. Fish and Wildlife Service, Laurel, Maryland.

Fimreite, N. 1971. Effects of Dietary Methylmercury on Ring-necked Pheasants. Canadian Wildlife Service

Occasional Paper 9. H. T. Harvey & Associates. 2010. San Joaquin River Water Quality Improvement Project, Phase I Wildlife

Monitoring Report 2009. Prepared for Panoche Drainage District. H. T. Harvey & Associates. 2011. San Joaquin River Water Quality Improvement Project, Phase I Wildlife

Monitoring Report 2010. Prepared for Panoche Drainage District. H. T. Harvey & Associates. 2012. San Joaquin River Water Quality Improvement Project, Phase I Wildlife

Monitoring Report 2011. Prepared for Panoche Drainage District. Heinz G., D. J. Hoffman, J. Klimstra, K. Stebbins, S. Konrad, and C. Erwin. 2009. Species differences in the

sensitivity of avian embryos to methylmercury. Archives of Environmental Contamination and Toxicology 56:129–138.

Kennamer, R. A., J. R. Stout, B. P. Jackson, S. V. Colwell, I. L. Brisbin, and J. Burger. 2005. Mercury patterns

in wood duck eggs from a contaminated reservoir in South Carolina, USA. Environmental Toxicology and Chemistry 24:1793–1800. Doi: 10.1897/03-661.1.

McCullagh, P., and J. A. Nelder. 1989. Generalized Linear Models. Second edition. Chapman and Hall,

London, England, and New York, NY. R Core Team. 2013. R: A language and environment for statistical computing. R Foundation for Statistical

Computing. Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org. [Service] U.S. Fish and Wildlife Service. 2003. Evaluation of the Clean Water Act Section 304(a) Human

Health Criterion for Methylmercury: Protectiveness for Threatened and Endangered Wildlife in California. Environmental Contaminants Division, Sacramento, CA.

Skorupa, J., and H. Ohlendorf. 1991. Contaminants in drainage water and avian risk thresholds. In A. Dinar

and D. Zilberman (Editors), The Economics and Management of Water and Drainage in Agriculture. Kluwer Academic Publishers.

Sokal R. R., and F. J. Rohlf. 1995. Biometry. W. H. Freeman and Company, New York, NY. Suter, G., II. 1996. Toxicological benchmarks for screening contaminants of potential concern for effects on

freshwater biota. Environmental Toxicology and Chemistry 15:1232–1241. Zar, J. H. 1999. Biostatistical Analysis. Prentice Hall, NJ.


Zuur, A. F., E. N. Ieno, N. J. Walker, A. A. Saveliev, and G. M. Smith. 2009. Mixed effects models and

extensions in ecology with R. Springer Science+Business Media, LLC, New York, NY.


Appendix A. Examination of Residuals for Final Statistical Models

2002 2006 2010

-3-2

-10

12

34

Year

Pea

rson

resi

dual

s s

Project Reference

-3-2

-10

12

34

Site

Pea

rson

resi

dual

s s

2002 2006 2010

-0.6

-0.2

0.2

0.6

Year

Dev

ianc

e re

sidu

als

Project Reference

-0.6

-0.2

0.2

0.6

Site

Dev

ianc

e re

sidu

als

Figure A1. Examination of residuals for the final model for killdeer, selenium analysis, which includes location, year3, and interaction terms.

1.1 1.2 1.3 1.4 1.5

-0.5

0.0

0.5

Fitted values

Res

idua

ls

Residuals vs Fitted

294147

439

Residuals

Freq

uenc

y

-0.5 0.0 0.5

010

2030

4050

2004 2008 2012

-0.6

-0.2

0.2

0.6

Year

Res

idua

ls

Project Reference

-0.6

-0.2

0.2

0.6

Site

Res

idua

ls

Figure A2. Examination of residuals for the final model for recurvirostrids, selenium analysis, which includes location and year2.

2004 2008 2012

-10

12

Year

Pea

rson

resi

dual

s s

Project Reference

-10

12

Site

Pea

rson

resi

dual

s s

2004 2008 2012

-0.2

0.0

0.2

Year

Dev

ianc

e re

sidu

als

Project Reference

-0.2

0.0

0.2

Site

Dev

ianc

e re

sidu

als

Figure A3. Examination of residuals for the final model for red-winged blackbirds, selenium analysis, which includes location, year3, and interaction terms.

Figure A4. Examination of residuals for the final model for killdeer, boron analysis, which includes location, year2, and no interaction term.

2004 2008 2012

-10

12

3

Year

Pea

rson

resi

dual

s s

Project Reference

-10

12

3

Site

Pea

rson

resi

dual

s s

2004 2008 2012

-2.0

-1.0

0.0

1.0

Year

Dev

ianc

e re

sidu

als

Project Reference

-2.0

-1.0

0.0

1.0

Site

Dev

ianc

e re

sidu

als

Figure A5. Examination of residuals for the final model for recurvirostrids, boron analysis, which includes year2.

0.4 0.6 0.8 1.0

-20

24

Fitted values

Nor

mal

ized

resi

dua

Normalized residuals

Freq

uenc

y

-4 -2 0 2 4

020

4060

80

2004 2008 2012

-20

24

Year

Nor

mal

ized

resi

dual

Project Reference

-20

24

Site

Nor

mal

ized

resi

dual

Figure A6. Examination of residuals for the final model for red-winged blackbirds, boron analysis, which includes location, year2, and interaction terms.

Figure A7. Examination of residuals for the final model for vegetation selenium analysis, which includes location and year (as a factor).

0.1 0.2 0.3 0.4 0.5 0.6

-2-1

01

23

Fitted values

Nor

mal

ized

resi

dual


Freq

uenc

y

-2 -1 0 1 2 3

05

1015

2025

2008 2009 2010 2011 2012

-2-1

01

23

Year

Nor

mal

ized

resi

dual

Project Reference

-2-1

01

23

Site

Nor

mal

ized

resi

dual

Figure A8. Examination of residuals for the final model for small mammals, selenium analysis, which includes location.

0.4 0.5 0.6 0.7

-2-1

01

23

Fitted values

Nor

mal

ized

resi

dual


Freq

uenc

y

-2 -1 0 1 2 3

05

1015

2025

2008 2009 2010 2011 2012

-2-1

01

23

Year

Nor

mal

ized

resi

dual

Project Reference

-2-1

01

23

Site

Nor

mal

ized

resi

dual


Appendix B. 2012 Killdeer Egg-boron Concentrations at the San Joaquin River Water Quality Improvement Project

2012 Killdeer Egg-boron Concentrations at the San Joaquin River Water Quality Improvement Project

Eastern Project Area Reference Area

ID Number

Boron (ppm, dry wt)a

Log Base 10 Anti-log ID

Number Boron

(ppm, dry wt) a Log

Base 10 Anti-log

01 3.85 0.5855 01 1.14 0.0569

02 0.314 -0.5031 02 0.035b -1.4559

03 3.75 0.5740 03 0.441 -0.3556

04 2.56 0.4082 04 0.227 -0.6440

05 3.32 0.5211 05 0.802 -0.0958

06 1.73 0.2380 06 1.97 0.2945

07 0.615 -0.2111 07 1.58 0.1987

08 0.873 -0.0590

09 1.25 0.0969

10 0.864 -0.0635

Arith./Geo. Mean 2.31 0.2304 1.7 Arith./Geo. Mean 1.14 -0.2027 0.63

SD 1.5 0.4269 2.7 SD 0.6 0.5170 3.3

SE 0.1909 1.6 SE 0.2312 1.7

95% CI -0.1438 0.7 95% CI

-0.6558 0.2

0.6045 4.0 0.2505 1.8 Notes: CI = confidence interval; SD = standard deviation; SE = standard error. a ppm, dry wt = parts per million, dry weight. b A value of one half of the detection limit is substituted for samples that were below the detection limit.


Appendix C. 2012 Recurvirostrid Egg-boron Concentrations at the San Joaquin River Water Quality Improvement Project

2012 Recurvirostrid Egg-boron Concentrations at the San Joaquin River Water Quality Improvement Project

Eastern Project Area Reference Area Mitigation Site

ID Number Boron (ppm, dry wt) a

Log Base 10 Anti-log ID Number Boron

(ppm, dry wt)a Log

Base 10 Anti-log ID Number

Boron (ppm, dry wt)a


01 4.02 0.6042 01 0.035b -1.4559

02 0.912 -0.0400 02 0.106 -0.9747

03 20.4 1.3096 03 0.148 -0.8297

04 0.663 -0.1785 04 0.784 -0.1057

05 0.181 -0.7423 05 20.3 1.3075

06 1.71 0.2330

07 8.71 0.9400

08 0.406 -0.3915

09 0.549 -0.2604

10 1.54 0.1875

Arith./Geo. Mean Arith./Geo. Mean 3.91 0.1662 1.5 Arith./Geo. Mean 4.3 -0.4117 0.39

SD SD 6.35 0.6309 4.3 SD 9.0 1.0760 11.9

SE SE 0.2822 1.9 SE 0.4812 3.0

95% CI 95% CI -0.3869 0.4 95% CI

-1.3549 0.0



Appendix D. 2012 Red-winged Blackbird Egg-boron Concentrations at the San Joaquin River Water Quality Improvement Project


2012 Red-winged Blackbird Egg-boron Concentrations at the San Joaquin River Water Quality Improvement Project


ID Number Boron (ppm, dry wt)a

Log Base 10 Anti-log ID Number Boron

(ppm, dry wt)a Log

Base 10 Anti-log

01 13.3 1.1239 01 2.52 0.4014

02 8.84 0.9465 02 3.66 0.5635

03 9.45 0.9754 03 2.15 0.3324

04 19.2 1.2833 04 3.31 0.5198

05 10.9 1.0374 05 1.89 0.2765

06 7.12 0.8525 06 1.24 0.0934

07 5.70 0.7559 07 0.238 -0.6234

08 4.57 0.6599 08 0.775 -0.1107

09 5.11 0.7084 09 0.035b -1.4559

10 5.52 0.7419 10 0.820 -0.0862

11 8.21 0.9143 11 1.30 0.1139

Arith./Geo. Mean 8.90 0.9090 8.1 Arith./Geo. Mean 1.63 0.0022 1.0

SD 4.34 0.1912 1.6 SD 1.19 0.5904 3.9

SE 0.0855 1.2 0.2640 1.8

95% CI 0.7415 5.5

-0.5152 0.3



Appendix E. 2012 Killdeer Egg-mercury Concentrations at the San Joaquin River Water Quality Improvement Project


2012 Killdeer Egg-mercury Concentrations at the San Joaquin River Water Quality Improvement Project

Eastern Project Area Reference Area

ID Number

Mercury Log Base 10 Anti-log ID

Number Mercury Log

Base 10 Anti-log (ppm, wet wt)a (ppb, dry wt)b (ppm, wet wt)a (ppb, dry wt)b

01 0.0682 257 2.4099 01 0.0769 291 2.4639

02 0.0948 330 2.5185 02 0.0712 268 2.4281

03 0.170 619 2.7917 03 0.0531 195 2.2900

04 0.0752 296 2.4713 04 0.0844 320 2.5051

05 0.188 718 2.8561 05 0.0694 265 2.4232

06 0.213 818 2.9128 06 0.0822 311 2.4928

07 0.123 471 2.6730 07 0.0956 364 2.5611

08 0.107 381 2.5809

09 0.056 201 2.3032

10 0.144 519 2.7152

Arith./Geo. Mean 0.133/0.122 501.29 2.6619 459 Arith./Geo. Mean 0.084/0.081 311.50 2.4764 299

SD 0.058 221.1 0.1992 1.6 SD 0.027 94.9 0.1275 1.3

SE 0.0891 1.2 SE 0.0570 1.1

95% CI 2.4873 307.1 95% CI

2.3646 231.5

2.8365 686.2 2.5881 387.3 Notes: CI = confidence interval; SD = standard deviation; SE = standard error. a ppm, wet wt = parts per million, wet weight. b ppb, dry wt = parts per billion, dry weight.


Appendix F. 2012 Recurvirostrid Egg-mercury Concentrations at the San Joaquin River Water Quality Improvement Project

2012 Recurvirostrid Egg-mercury Concentrations at the San Joaquin River Water Quality Improvement Project

Eastern Project Area Reference Area Mitigation Site

ID Number

Mercury Log Base

10

Anti-log

ID Number

Mercury Log

Base 10 Anti-log ID Number

Mercury Log Base

10

Anti-log (ppm, wet

wt)a (ppb, dry

wt)b (ppm, wet wt)a (ppb, dry wt)b (ppm, wet wt)a (ppb, dry wt)b

01 0.427 1770 3.2480 01 0.3500 1430 3.1553

02 0.379 1440 3.1584 02 0.4050 1720 3.2355

03 0.0918 369 2.5670 03 0.1990 736 2.8669

04 0.150 585 2.7672 04 0.0620 231 2.3636

05 0.116 465 2.6675 05 0.0677 264 2.4216

06 0.230 926 2.9666

07 0.0826 329 2.5172

08 0.830 3370 3.5276

09 0.228 895 2.9518

10 0.239 967 2.9854

Arith./Geo. Mean Arith./Geo. Mean 0.277/0.216 1111.6 2.9357 862 Arith./Geo.

Mean 0.217/0.164 876.2 2.8086 644

SD SD 0.226 919.1 0.3184 2.1 SD 0.158

676.3 0.4042 2.5

SE SE 0.1424 1.4 SE 0.1808 1.5

95% CI 95% CI 2.6566 453.5 95% CI

2.4543 284.6



Appendix G. 2012 Red-winged Blackbird Egg-mercury Concentrations at the San Joaquin River Water Quality Improvement Project

2012 Red-winged Blackbird Egg-mercury Concentrations at the San Joaquin River Water Quality Improvement Project


ID Number

Mercury Log Base 10 Anti-log ID

Number Mercury Log

Base 10 Anti-log (ppm, wet wt)a (ppb, dry wt)b (ppm, wet wt)a (ppb, dry wt)b

01 0.0485 313 2.4955 01 0.0124 97.7 1.9899

02 0.0103 69.0 1.8388 02 0.0154 115.0 2.0607

03 0.0457 325 2.5119 03 0.0141 97.9 1.9908

04 0.0136 129 2.1106 04 0.00661 43.8 1.6415

05 0.00908 80.9 1.9079 05 0.0160 77.3 1.8882

06 0.0393 274 2.4378 06 0.01470 152 2.1818

07 0.0658 447 2.6503 07 0.0131 104 2.0170

08 0.0384 298 2.4742 08 0.0149 128 2.1072

09 0.0113 84.9 1.9289 09 0.0231 169 2.2279

10 0.0248 185 2.2672 10 0.00990 62.4 1.7952

11 0.0233 169 2.2279 11 0.0367 239 2.3784

Arith./Geo. Mean 0.030/0.024 215.9 2.2592 182 Arith./Geo. Mean 0.016/0.015 116.9 2.0253 106

SD 0.019 123.5 0.2798 1.9 SD 0.008 54.6 0.2049 1.6

SE 0.1251 1.3 SE 0.0916 1.2

95% CI 2.0139 103.3 95% CI

1.8457 70.1



Appendix H. 2012 Control Eggs, Selenium Results


2012 Control Eggs, Selenium Duplicate Results

ID Number Replication Selenium (ppm, dry wt)a

PK-1 1 19.8

2 18.7

SD 0.7778

PK-2 1 17.9

2 17.0

SD 0.6364

PK-3 1 40.8

2 45.2

SD 3.1113

PK-4 1 33.5

2 31.8

SD 1.2021

PB-2 1 6.12

2 6.52

SD 0.2828

WL-5 1 7.63

2 7.74

SD 0.0778

PK-1 1 19.8

2 18.7

SD 0.7778

PK-2 1 17.9

Mean SD: 1.0147

Low SD: 0.0778

High SD: 3.1113 Notes: SD = standard deviation. a ppm, dry wt = parts per million, dry weight.


Appendix I. 2012 Control Eggs, Boron Results


Boron Control Spikes

ID Number Tissue Spiked

Boron (mg) %

Recovery

PDD-P-K-02 Egg 0.1 105

PDD-P-K-06 Egg 0.1 102

PDD-R-R-08 Egg 0.1 101

PDD-M-05 Egg 0.1 102

Mean: 102.5

SD: 1.7 Notes: SD = standard deviation.


2012 Control Eggs, Boron Duplicate Results

ID Number Replication Boron (ppm, dry wt)a

ID Number Replication Boron (ppm, dry wt)

PK-1 1 1.00 RR-6 1 0.410

2 1.04 2 0.440

SD 0.0283 SD 0.0212

PK-5 1 0.900 RR-7 1 2.15

2 0.840 2 2.22

SD 0.0424 SD 0.0495

RK-6 1 0.420 RR-8 1 0.110

2 0.540 2 0.090

3 0.600 SD 0.0141

SD 0.0917 PDDM-2 1 0.050

RK-7 1 0.380 2 0.00

2 0.450 SD 0.0354

SD 0.0495 PDDM-4 1 0.150

RK-8 1 0.170 2 0.270

2 0.320 SD 0.0849

SD 0.1061 PDDM-5 1 5.35

RR-5 1 0.050 2 5.08

2 0.040 SD 0.1909

SD 0.0071

Mean SD: 0.0601

Low SD: 0.0071

High SD: 0.1909 Notes: SD = standard deviation. a ppm, dry wt = parts per million, dry weight.


Appendix J. 2012 Control Eggs, Mercury Results


2012 Control Eggs, Mercury Duplicate Results

ID Number Replication Result Mercury ID Number Replication Result

Mercury

PK-2 1 94.9 RR-9 1 221

2 94.6 2 235

SD 0.212 SD 9.899

PK-7 1 121 PDM-10 1 354

2 124 2 345

SD 2.121 SD 6.364

RR-2 1 382 RR-9 1 221

2 375 2 235

SD 4.950 SD 9.899

RR-3 1 89.6

2 94.0

SD 3.111

Mean SD: 6.839

Low SD: 0.212

High SD: 21.213 Notes: SD = standard deviation.


Appendix K. Killdeer and Recurvirostrid Nest Survey Results for the San Joaquin River Water Quality Improvement Eastern Project Area and Pilot Mitigation Sites

Killdeer Nest Survey Results for the San Joaquin River Water Quality Improvement Eastern Project Area

Field Strata Date No. of

Eggs Date

No. of

Eggs Date

No. of

Eggs Date

No. of

Eggs Comments Nest

Status Nest Fate

Nest Agent

Killdeer 10-4 Field edge 5/4 2 5/7 0 Depredated 5 5 4 13-1 Palm trees 5/11 4 5/18 3 5/29 3 6/8 0 PK-1 collected 5/11, ph 1 4 1 12-3 Road edge 5/15 1 5/22 0 Farm implement 5 5 7 14-3 Orchard 5/22 3 5/29 0 Depredated 5 5 4

13-6 Road edge 6/4 2 6/8 4 6/14 0 PK-2 collected 6/8, farm implement 5 5 7

3-5 Road 6/14 4 6/20 3 6/29 3 7/13 0 PK-3 collected 6/14, ph 1 4 1 13-4 Road edge 6/14 4 6/20 3 6/29 3 7/13 0 PK-4 collected 6/14, ph 1 4 1 18-2 Road edge 6/18 3 6/20 4 6/29 0 PK-5 collected 6/20, depredated 5 5 4

17-1 Near pump 6/20 4 6/29 0 PK-6 collected 6/20, farm implement 5 5 7

13-6 Road edge 6/27 3 6/29 4 7/13 0 PK-7 collected 6/29, farm implement 5 5 7

Codes for nest status, nest fate, and nest agent: Nest status: Nest fate: Nest agent: Abbreviations used in comment column: 1 Undisturbed/normal 1 Lost (not relocated) 1 None fth = Egg that has failed to hatch. 2 Investigator damaged 2 Fate uncertain 2 Unknown ph = Presumed hatched. 3 Partially destroyed 3 Hatched (certain) 3 Observer 4 Some eggs missing 4 Presumed hatched 4 Predator 5 Totally destroyed 5 Destroyed 5 Livestock 6 Other (poachers, etc.) 6 Abandoned 6 Flooding 7 Past term/unviable 7 Vehicle 8 Terminated 8 Levee maintenance

Killdeer and Recurvirostrid Nest Survey Results for the San Joaquin River Water Quality Improvement Mitigation Site

Nest ID Cell Strata Date

No. of

Eggs Date

No. of

Eggs Date

No. of

Eggs Date

No. of

Eggs Comments Nest

Status Nest Fate

Nest Agent

Killdeer 001 3 Levee 5/24 3 6/12 4 6/18 4 6/27 0 ph 1 4 1 002 4 Levee 6/1 4 6/12 4 6/18 4 6/27 0 ph 1 4 1 003 2 Levee 6/27 4 6/12 4 6/18 4 6/27 0 ph 1 4 1

Black-necked stilt 001 3 Long island 5/24 2 5/29 0 Depredated 5 5 4 002 3 Long island 5/24 3 5/29 0 Depredated 5 5 4 003 3 Long island 5/24 2 5/29 0 Depredated 5 5 4 004 2 Mudflat 6/1 4 6/12 3 6/18 3 6/27 0 PDM-1 collected 6/1, ph 1 4 1 005 4 Mudflat 6/4 4 6/12 4 6/18 4 6/27 0 Chicks nearby 6/24, ph 1 4 1

006 4 Mudflat 6/12 4 6/18 4 6/27 4 7/13 0 Adult with chicks nearby, ph 1 4 1

American avocet 001 3 Long island 5/24 2 5/29 0 Depredated 5 5 4 002 3 Long island 5/24 1 5/29 0 Depredated 5 5 4 003 3 Long island 5/24 4 5/29 0 Depredated 5 5 4 004 3 Long island 5/24 1 5/29 0 Depredated 5 5 4 005 3 Long island 5/24 2 5/29 0 Depredated 5 5 4 006 3 Long island 5/24 1 5/29 0 Depredated 5 5 4 007 3 Long island 5/24 2 5/29 0 Depredated 5 5 4 008 2 Small island 5/24 4 5/29 4 6/4 4 6/12 0 PDM-2 collected 6/4, ph 1 4 1 009 4 Mudflat 6/4 4 6/12 3 6/18 3 6/27 0 PDM-3 collected 6/4, ph 1 4 1 010 4 Mudflat 6/4 4 6/12 3 6/18 3 6/27 0 PDM-4 collected 6/4, ph 1 4 1 011 4 Mudflat 6/4 4 6/12 3 6/18 3 6/27 0 PDM-5 collected 6/4, ph 1 4 1



Codes for nest status, nest fate, and nest agent: Nest status: Nest fate: Nest agent: Abbreviations used in comment column: 1 Undisturbed/normal 1 Lost (not relocated) 1 None fth = Egg that has failed to hatch. 2 Investigator damaged 2 Fate uncertain 2 Unknown ph = Presumed hatched. 3 Partially destroyed 3 Hatched (certain) 3 Observer 4 Some eggs missing 4 Presumed hatched 4 Predator 5 Totally destroyed 5 Destroyed 5 Livestock 6 Other (poachers, etc.) 6 Abandoned 6 Flooding 7 Past term/unviable 7 Vehicle 8 Terminated 8 Levee maintenance

san joaquin river water quality …...san joaquin river h. t. harvey & associates water quality...

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