Table of Contents LIST OF FIGURES IV LIST OF TABLES XI PROJECT SUMMARY 1 ACKNOWLEDGEMENTS 3 1.0 INTRODUCTION 5 1.1 Project Scope 5 1.2 Geographic Setting 6 1.3 Project background 7 1.4 Report Organization 10 2.0 LITERATURE REVIEW 11 3.0 THE 2011-2017 EMERALD BAY NATURAL PERTURBATION 16 4.0 FIELD MEASUREMENTS ASSOCIATED WITH THIS STUDY 18 4.1 Synoptic Surveys of Mysis and Zooplankton 21 4.1.1 Methods 21 4.1.2 Emerald Bay Results 22 4.1.3 Lake Tahoe Results 33 4.2 Biosonics Echosounder Surveys 35 4.2.1 Methods 35 4.2.2 Emerald Bay Results 41 4.2.3 Lake Tahoe Results 45 4.2.4 Biosonics Conclusions 51 4.3 Water Quality 52 4.3.1 Emerald Bay 52 4.3.2 Lake Tahoe 55 4.4 Physical Profiling 59 4.4.1 Emerald Bay 59 4.4.2 Lake Tahoe 60 i 4.4.3 Summary of Physical and Water Quality Variables in Emerald Bay and Lake Tahoe 62 4.5 Phytoplankton 63 4.5.1 Phytoplankton in Emerald Bay 63 4.5.2 Phytoplankton in Lake Tahoe 68 4.5.3 Comparison between phytoplankton in Lake Tahoe’s main basin and Emerald Bay 71 4.6 Thermistor Chain data 71 5.0 EMERALD BAY TRAWLING RESULTS 73 5.1 Description of Trawl and Net Modifications 73 5.2 Trawling Schedule and Operations 77 5.3 Catch per Unit Effort 80 5.4 Bycatch 81 5.5 Scaling up to Commercial Harvest 82 6.0 EXPERIMENT TO COMPARE AND CONTRAST THE INFLUENCE OF INVASIVE MYSID SHRIMP AND NATIVE ZOOPLANKTON ON THE PROPERTIES OF THE PELAGIC ENVIRONMENT OF LAKE TAHOE AND EMERALD BAY 84 6.1 Materials & Methods 85 6.1.1 Phytoplankton concentrations, grazing indices, and PPR 86 6.1.2 Particle concentrations 87 6.1.3 Nutrient concentrations 88 6.1.4 Statistical Analyses 88 6.2 Results 89 6.2.1 Lake Tahoe 89 6.2.2 Emerald Bay 90 6.2.3 Comparisons between Lake Tahoe and Emerald Bay 91 6.3 Discussion 91 7.0 QUANTIFY THE FEEDING BEHAVIOR OF MYSIDS IN TWO LOCATIONS, EMERALD BAY AND LAKE TAHOE FROM EARLY AND LATE SUMMER 104 7.0.1 Diet Analysis 104 7.0.2 Stable Isotope Analyses 104 7.1 Results 105 7.1.1 Diet analysis 105 7.1.2 Stable isotope analysis 106 ii 7.2 Discussion 111 8.0 SUMMARY OF LESSONS LEARNED FROM EMERALD BAY AND LAKE TAHOE: 2018-2020 113 9.0 A 15-YEAR LAKE TAHOE MYSIS CONTROL PLAN 123 9.1 The Plan 124 9.1.1 Phase I: Control Emerald Bay Mysis Population 125 9.1.2 Phase II: Monitor Emerald Bay and Commence Commercial Trawling in Lake Tahoe 126 9.1.3 Phase III: Reduce Tahoe Mysis Population Density to 27 ind./m2 128 9.2 Cost Projections 129 9.4. Concomitant Monitoring and Research Needs 130 9.5. Science and Monitoring Timeline 130 10.0 REFERENCES 132 11.0 APPENDIX 1 140 iii List of Figures Figure Caption Page 2.1 Time series of population counts (ind./m2) for Daphnia, Bosmina, Epischura and 12 Diaptomus from 1967-1973 following the introduction of Mysis (from Richards et al. 1975). 2.2 Primary productivity in Lake Tahoe. The dates of Mysis introduction and the last 13 comprehensive study of Mysis in Emerald Bay (Morgan (1979) are shown. 2019 data are considered provisional. 2.3 Annual Secchi depth in Lake Tahoe. The dates of Mysis introduction and the last 14 comprehensive study of Mysis in Emerald Bay (Morgan 1979) are shown. 3.1 Secchi depth and Mysis shrimp and Zooplankton abundance in Emerald Bay. Top: 16 Secchi depth (m) in Emerald Bay, Bottom: Mysis shrimp abundance in number of ind./m2 shown as red circle, Daphnia spp. and Bosmina spp. abundance in number of ind./m3 are shown in blue and green circles, respectively. Mysis abundance can be converted to a volumetric basis by dividing by the sampling depth of 60 m. 4.1 Mysis monitoring sites maintained from 2018-2019 (red triangles). Yellow star is the 18 location of a thermistor chain station installed in Emerald Bay. Yellow circle is Buoy TB3 where overnight Biosonics surveys were conducted. Depth contours shown at 20 m intervals (gray) to 120 m depth, and at 50 m intervals (black) from 150 m to 450 m. MLTP and LTP are the two long-term monitoring stations maintained by UC Davis. 4.2 Mysis shrimp and Zooplankton abundance in Emerald Bay. Mysis shrimp abundance 22 in number of individuals per square meter shown as red circle, Daphnia spp. and Bosmina spp. abundance in number of individuals per cubic meter are shown in blue and green circles, respectively. Mysis abundance can be converted to a volumetric basis by dividing by the sampling depth of 60 m. 4.3 Percentage of female Mysis population that is reproductive. 23 4.4 Percentage of male Mysis population that is reproductive. 23 4.5 Reproductive vs non-reproductive Mysis females in Emerald Bay. 24 iv 4.6 Reproductive vs non-reproductive Mysis females in Lake Tahoe. 24 4.7 Mysis eggs just after appearance in brood pouch. 28 4.8 Stage 1 of Mysis development within brood pouch. 28 4.9 Stage 2 of Mysis development within brood pouch. 29 4.10 Stage 3 of Mysis development within brood pouch. 29 4.11 Stage 5 of Mysis development within brood pouch. 30 4.12 Stage 6 of Mysis development within brood pouch. 30 4.13 Nine additional sampling stations established in Emerald Bay in late 2018 to monitor 31 seasonal movement of Mysis at various life stages throughout the bay. Station 4 is the long-term monitoring station for Emerald Bay maintained since 2011. 4.14 Average Mysis density at shallow sites (depth <30m, n = 4) and deep sites (depth 32 >30m, n = 6). 4.15 Zooplankton density in Emerald Bay, 2017-2019. 33 4.16 Mysis shrimp and zooplankton abundance at Index station (LTP) in Lake Tahoe. 34 Mysis shrimp abundance in number of individuals per square meter shown by red circles, Daphnia and Bosmina abundance in number of individuals per cubic meter are shown in blue and green circles, respectively. Mysis abundance can be converted to a volumetric basis by dividing by the sampling depth of 100 m. 4.17 Zooplankton abundance at the Index Station (LTP), 2018-2019. 34 4.18 Biosonics DT-X Extreme Split-beam Echosounder being attached to the R/V Bob 35 Richards (February, 2018). 4.19 Processing flow chart for analysis of the raw datafiles collected using the Biosonics 37 sonar. v 4.20 Regression of observed Field Density vs. Prediction Density for: (a) April 3, 2019 38 and (b) October 7, 2019. Units for both axes are # of individuals per square meter. 4.21 Measured vertical migration rates of Mysis for a typical night (March 28, 2018) at 41 (a) the beginning of the night, (b) late night, and (c) early morning as they start undergoing their descent. Data are from Lake Tahoe. 4.22 (a) and (c) show two representative transects collected on August 13, 2018 with the 43 depth of the thermocline shown with a solid horizontal line ~10 m depth. (b) and (d) show the vertical profiles of concentration through the deepest section of each transect. While the individuals are bounded at the surface, they spread in a relatively diffuse cloud in the region beneath. 4.23 Full synoptic mapping of Emerald Bay on (a) March 19, 2018; (b) June 6, 2018; (c) 44 August 13, 2018; and, (d) October 23, 2018. The range on the color bar is from 0- 200 individuals/m2 in each of the subpanels in order to be consistent throughout. 4.24 Full synoptic mapping of Emerald Bay on (a) March 18, 2019; (b) June 10, 2019; (c) 45 August 12, 2019; and (d) December 9, 2019. The range on the color bar is from 0- 200 individuals/m2 in each of the subpanels in order to be consistent throughout. 4.25 (a) Backscatter return from a single transect on August 27, 2019 in the main body of 46 Lake Tahoe (shown in blue) after removing the surface backscatter return and clipping the data at 150 m (greater than this tends to generate false positives at depth with depth of the thermocline (black horizontal line). (b) Vertical profile of average volumetric density (individuals/m3) with depth with depth of the thermocline (black horizontal line) indicated. The length of the transect shown is approximately 4 km. 4.26 (a) Backscatter return from a single transect on September 17, 2018 in the main body 47 of Lake Tahoe (shown in blue) starting on shore at Camp Richardson and then turning around and returning to shore around Ping 1500 after removing the surface backscatter return and clipping the data at 150 m. Depth of the thermocline shown as a black horizontal line. (b) Vertical profile of average volumetric density (individuals/m3) with depth with depth of the thermocline (black horizontal line) indicated. 4.27 Paired cross-lake transects across the northern end of Lake Tahoe on (a) July 10, 48 2018; (b) September 19, 2018; (c) November 13, 2018; (d) March 19, 2019; (e) August 27, 2019; and, (f) December 17, 2019. The limits on the color bar range from 0-200 individuals/m2 in each of the subpanels. vi 4.28 On-shore/offshore transects collect at Camp Richardson on (a) Sept. 17, 2018; (b) 50 March 18, 2019; (c) June 6, 2019; and (d) August 12, 2019 showing the relative density of individual Mysis at this site.