Biological and Conference Opinion Issuance of a Section 10(a)(1)(B) Permit for the Santa Clara Valley Habitat Conservation Plan/Natural Community Conservation Plan April 2013 File Number 81420-2009-F-0077 U.S. Fish and Wildlife Service Sacramento Fish and Wildlife Office Endangered Species Division 2800 Cottage Way, Room W-2605 Sacramento, California 95825-1846 TABLE OF CONTENTS 1. CONSULTATION HISTORY .............................................................................................. 4 2. BIOLOGICAL OPINION AND CONFERENCE OPINION ............................................... 6 2.1 Description of the Proposed Action .............................................................................. 6 2.1.1 Covered Species .............................................................................................. 6 2.1.2 Permit Area ...................................................................................................... 6 2.1.3 Permit Term ..................................................................................................... 7 2.1.4 Covered Activities ........................................................................................... 7 2.1.5 Conditions on Covered Activities ................................................................. 11 2.1.6 Effects ............................................................................................................ 12 2.1.7 Conservation Strategy ................................................................................... 14 2.1.8 Monitoring and Adaptive Management ........................................................ 22 2.1.9 Cost ................................................................................................................ 25 2.1.10 Funding .......................................................................................................... 25 2.1.11 Implementation .............................................................................................. 27 2.2 Action Area ................................................................................................................. 30 2.3 Analytical Framework for the Jeopardy and Adverse Modification Analysis ........... 31 2.3.1 Jeopardy Determination ................................................................................ 31 2.3.2 Adverse Modification Determination ............................................................ 31 2.4 Serpentine Species ...................................................................................................... 32 2.4.1 Status of the Species/Critical Habitat ............................................................ 32 2.4.1.1 Bay Checkerspot Butterfly ............................................................ 33 2.4.1.2 Tiburon Indian Paintbrush ............................................................ 36 2.4.1.3 Coyote Ceanothus ......................................................................... 36 2.4.1.4 Mount Hamilton Thistle ................................................................ 36 2.4.1.5 Santa Clara Valley Dudleya .......................................................... 38 2.4.1.6 Fragrant Fritillary .......................................................................... 38 2.4.1.7 Smooth Lessingia .......................................................................... 39 2.4.1.8 Metcalf Canyon Jewelflower ........................................................ 40 2.4.1.9 Most Beautiful Jewelflower .......................................................... 40 2.4.2 Environmental Baseline ................................................................................ 41 2.4.2.1 Bay Checkerspot Butterfly ............................................................ 42 2.4.2.2 Tiburon Indian Paintbrush ............................................................ 44 2.4.2.3 Coyote Ceanothus ......................................................................... 45 2.4.2.4 Mount Hamilton Thistle ................................................................ 45 2.4.2.5 Santa Clara Valley Dudleya .......................................................... 46 2.4.2.6 Fragrant Fritillary .......................................................................... 47 2.4.2.7 Smooth Lessingia .......................................................................... 49 2.4.2.8 Metcalf Canyon Jewelflower ........................................................ 50 2.4.2.9 Most Beautiful Jewelflower .......................................................... 51 2.4.3 General Effects of the Action on All Covered Species ................................. 52 2.4.3.1 Mortality, Injury, Harm, and Harassment ..................................... 53 2.4.3.2 Plant Habitat Loss and Degradation ............................................. 62 2.4.3.3 Habitat Fragmentation .................................................................. 63 2.4.3.4 Disease .......................................................................................... 65 2.4.3.5 Nonnative Invasives ...................................................................... 66 2.4.3.6 Noise ............................................................................................. 69 2.4.3.7 Lighting ......................................................................................... 70 2.4.3.8 Dust ............................................................................................... 71 2.4.3.9 Fire ................................................................................................ 73 2.4.3.10 Capture and Collection ................................................................. 75 2.4.4 General Effects of the Action on Serpentine Species .................................... 76 2.4.5 Species-Specific Effects of the Action .......................................................... 82 2.4.5.1 Bay Checkerspot Butterfly ............................................................ 83 2.4.5.2 Tiburon Indian Paintbrush ............................................................ 95 2.4.5.3 Coyote Ceanothus ......................................................................... 97 2.4.5.4 Mount Hamilton Thistle .............................................................. 101 2.4.5.5 Santa Clara Valley Dudleya ........................................................ 105 2.4.5.6 Fragrant Fritillary ........................................................................ 110 2.4.5.7 Smooth Lessingia ........................................................................ 112 2.4.5.8 Metcalf Canyon Jewelflower ...................................................... 116 2.4.5.9 Most Beautiful Jewelflower ........................................................ 119 2.4.6 Cumulative Effects ...................................................................................... 122 2.4.6.1 Climate Change ........................................................................... 123 2.4.6.2 Nitrogen Deposition .................................................................... 125 2.4.7 Conclusion ................................................................................................... 126 2.5 Aquatic Species ......................................................................................................... 126 2.5.1 Status of the Species/Critical Habitat .......................................................... 126 2.5.1.1 California Tiger Salamander (Central California DPS) .............. 126 2.5.1.2 California Red-Legged Frog ....................................................... 135 2.5.1.3 Foothill Yellow-Legged Frog ..................................................... 141 2.5.1.4 Western Pond Turtle ................................................................... 143 2.5.2 Environmental Baseline .............................................................................. 145 2.5.2.1 California Tiger Salamander (Central California DPS) .............. 145 2.5.2.2 California Red-Legged Frog ....................................................... 148 2.5.2.3 Foothill Yellow-Legged Frog ..................................................... 151 2.5.2.4 Western Pond Turtle ................................................................... 152 2.5.3 General Effects of the Action on Aquatic Species ...................................... 153 2.5.4 Species-Specific Effects of the Action ........................................................ 181 2.5.4.1 California Tiger Salamander (Central California DPS) .............. 181 2.5.4.2 California Red-Legged Frog ....................................................... 189 2.5.4.3 Foothill Yellow-Legged Frog ..................................................... 195 2.5.4.4 Western Pond Turtle ................................................................... 199 2.5.5 Cumulative Effects ...................................................................................... 202 2.5.6 Conclusion ................................................................................................... 203 2.6 Avian Species............................................................................................................ 203 2.6.1 Status of the Species .................................................................................... 203 2.6.1.1 Western Burrowing Owl ............................................................. 203 2.6.1.2 Least Bell’s Vireo ......................................................................