NATIONAL MARINE FISHERIES SERVICE ENDANGERED SPECIESACT SECTION 7 BIOLOGICAL OPINION Title: Biological Opinion on the Smalltooth Sawfish(Pristis pectinata) Research Permit Program Consultation Conducted By: EndangeredSpecies Act Interagency Cooperation Division, Officeof Protected Resources, National Marine Fisheries Service Action Agency: Permits and Conservation Division, Officeof Protected Resources, National Marine Fisheries Service Publisher: Officeof Protected Resources, National Marine Fisheries Service, National Oceanicand Atmospheric Administration, U.S. Department of Commerce Approved: , Donna S. Wieting Director, Officeof Protected Resour s FEB 1 4 2019 Date: Consultation Tracking Number: FPR-2017-9236 Digital Object Identifier (DOI): 10.25923 This page left blank intentionally Smalltooth sawfish programmatic FPR-2017-9236 TABLE OF CONTENTS Page 1 Introduction ........................................................................................................................... 1 1.1 Background ............................................................................................................. 2 1.2 Consultation History ............................................................................................... 2 2 Description of the Proposed Action ..................................................................................... 3 2.1 Application Submission and Review ...................................................................... 5 2.2 Analysis and Decision Making ............................................................................... 6 2.3 Legal Authorities, Policies, and Requirements for Permitting ............................... 6 2.3.1 Endangered Species Act (ESA) .............................................................................. 7 2.3.2 Regulatory Requirements for ESA Permits ............................................................ 7 2.4 Conservation and Recovery Benefits .................................................................... 15 2.5 Research Activities and Mitigation Measures ...................................................... 16 2.5.1 Capture Methods ................................................................................................... 16 2.5.2 Recaptures ............................................................................................................. 20 2.5.3 Research Techniques ............................................................................................ 20 2.6 Authorizing Capture, Handling, and Mortality ..................................................... 33 2.6.1 Assessing and Updating Abundance Estimates .................................................... 34 2.6.2 Authorizing Lethal Take of Smalltooth Sawfish .................................................. 36 2.6.3 Smalltooth Sawfish Mortality Limits.................................................................... 36 2.6.4 Mortality Limit Management ................................................................................ 38 2.6.5 Monitoring Actual Mortality................................................................................. 39 2.6.6 Exceeding Mortality Limits .................................................................................. 39 2.6.7 Expected Responses to Unintentional Mortality ................................................... 40 2.7 Adaptive Management Mechanisms ..................................................................... 41 2.8 Monitoring the Species Status of Smalltooth Sawfish .......................................... 42 2.9 Internal Program Review ...................................................................................... 42 2.10 Annual Reporting .................................................................................................. 43 2.11 Action Area ........................................................................................................... 44 2.11.1 Wild Smalltooth Sawfish ...................................................................................... 44 2.11.2 Captive Smalltooth Sawfish .................................................................................. 49 2.12 Interrealted and Interdependent Actions ............................................................... 50 3 The Assessment Framework .............................................................................................. 50 4 Status of Endangered Species Act Protected Resources ................................................. 52 4.1 Species and Critical Habitat Not Likely to be Adversely Affected ...................... 54 4.1.1 North Atlantic Right Whales and Their Designated Critical Habitat ................... 55 4.1.2 Other Large Whales .............................................................................................. 55 i Smalltooth sawfish programmatic FPR-2017-9236 4.1.3 Smalltooth Sawfish Designated Critical Habitat .................................................. 56 4.1.4 Shortnose Sturgeon ............................................................................................... 56 4.1.5 Gulf Sturgeon and Their Designated Critical Habitat ........................................... 56 4.1.6 Atlantic Sturgeon and Their Designated Critical Habitat ..................................... 57 4.1.7 Nassau Grouper ..................................................................................................... 57 4.1.8 Scalloped Hammerhead Shark .............................................................................. 58 4.1.9 Giant Manta Ray ................................................................................................... 58 4.1.10 Northwest Atlantic DPS Loggerhead Sea Turtle Critical Habitat ........................ 58 4.1.11 Elkhorn, Staghorn, and Reef Building Corals and Their Critical Habitat ............ 59 4.1.12 Johnsons Sea Grass and Its Designated Critical Habitat ...................................... 59 4.2 Species and Critical Habitat Likely to be Adversely Affected ............................. 60 4.2.1 Smalltooth Sawfish ............................................................................................... 60 4.2.2 Loggerhead Sea Turtles – Northwest Atlantic DPS ............................................. 63 4.2.3 Leatherback Sea Turtles ........................................................................................ 66 4.2.4 Hawksbill Sea Turtles ........................................................................................... 69 4.2.5 Kemp’s Ridley Sea Turtles ................................................................................... 72 4.2.6 Green Sea Turtles – North Atlantic DPS .............................................................. 74 4.2.7 Olive Ridley Sea Turtles ....................................................................................... 77 5 Environmental Baseline...................................................................................................... 80 5.1 Destruction of Mangrove and Reef Habitat .......................................................... 80 5.1.1 Agriculture ............................................................................................................ 80 5.1.2 Coastal and Urban Development .......................................................................... 81 5.2 Dredging ............................................................................................................... 82 5.3 Fisheries Bycatch .................................................................................................. 83 5.3.1 Smalltooth Sawfish Bycatch ................................................................................. 83 5.3.2 Sea Turtle Bycatch ................................................................................................ 84 5.4 Research ................................................................................................................ 86 5.5 Climate Change ..................................................................................................... 87 6 Effects of the Action ............................................................................................................ 90 6.1 Stressors Associated with the Proposed Action .................................................... 90 6.2 Mitigation to Minimize Response ......................................................................... 91 6.3 Exposure Analysis ................................................................................................ 92 6.3.1 Smalltooth Sawfish ............................................................................................... 92 6.3.2 Sea Turtles ............................................................................................................ 93 6.4 Response Analysis ................................................................................................ 94 6.4.1 Capture .................................................................................................................. 94 6.4.2 Effects of External and/or Minimally Invasive Implanted Tags ........................... 96 6.4.3 Effects of Genetic Clips and Muscle Biopsies ...................................................... 98 6.4.4 Effects of Blood Sampling .................................................................................... 98 6.4.5 Effects of Ultrasound ...........................................................................................