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CHSR Authority Merced to Fresno Plus Wye Section Reinitiation-2018

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CHSR Authority Merced to Fresno Plus Wye Section Reinitiation-2018 Refer to NMFS No: WCR--2018-10897/ WCRO-2018-00285 September 3, 2019 Mr. Mark McLoughlin Director of Environmental Services California High Speed Rail Authority 770 L Street Suite 620 Sacramento, California 95814 Re: Endangered Species Act Section 7(a)(2) Biological and Conference Opinion, and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Response, for the California High Speed Rail Merced to Fresno Section, including the Central Valley Wye Dear Mr. McLoughlin: Thank you for your letter of October 3, 2018, requesting re-initiation of formal consultation with NOAA’s National Marine Fisheries Service (NMFS) pursuant to Section 7 of the Endangered Species Act of 1973 (ESA) (16 U.S.C. 1531 et seq.) for California High Speed Rail Merced to Fresno Section, including the Central Valley Wye addition. The enclosed biological opinion is based on our review of the proposed action as detailed in the provided biological assessment, and its effects on the federally listed threatened California Central Valley steelhead (Oncorhynchus mykiss) distinct population segment and a nonessential experimental population of threatened Central Valley spring-run Chinook salmon (O. tshawytscha) evolutionarily significant unit, in accordance with Section 7 of the ESA. Based on the best available scientific and commercial information, NMFS concludes that the project is not likely to jeopardize the continued existence of the federally listed species, or jeopardize the reintroduction of nonessential experimental population Central Valley spring-run Chinook salmon into the San Joaquin River. NMFS has included an incidental take statement with reasonable and prudent measures and non-discretionary terms and conditions that are necessary and appropriate to avoid, minimize, or monitor the incidental take of federally listed fish that will occur with project implementation. Thank you, also, for your request for consultation pursuant to the essential fish habitat (EFH) provisions in Section 305(b) of the Magnuson-Stevens Fishery Conservation and Management Act (MSA)(16 U.S.C. 1855(b)) for this action. This biological opinion also includes NMFS’s review of the potential effects of the proposed action on EFH for Pacific Coast Salmon, as 2 designated under the MSA. The document concludes that the project will adversely affect the EFH of Pacific Coast Salmon in the action area and has included EFH Conservation Recommendations. As required by section 305(b)(4)(B) of the MSA, the Authority must provide a detailed response in writing to NMFS within 30 days after receiving an EFH Conservation Recommendation. Such a response must be provided at least 10 days prior to final approval of the action if the response is inconsistent with any of NMFS EFH Conservation Recommendations unless NMFS and the Authority have agreed to use alternative time frames for the Authority’s response. The response must include a description of measures proposed by the agency for avoiding, minimizing, mitigating, or otherwise offsetting the impact of the activity on EFH. In the case of a response that is inconsistent with the Conservation Recommendations, the Authority must explain its reasons for not following the recommendations, including the scientific justification for any disagreements with NMFS over the anticipated effects of the action and the measures needed to avoid, minimize, mitigate, or offset such effects (50 CFR 600.920(k)(1)). In your response to the EFH portion of this consultation, we ask that you clearly identify the number of Conservation Recommendations accepted. Please contact Katie Schmidt at the Central Valley Office in Sacramento at (916) 930-3685, or [email protected], if you have any questions concerning this consultation, or if you require additional information. Enclosure cc: To the File No. 151422-WCR2018-SA00467 John Hunter, [email protected] Chris Gurney, [email protected] Endangered Species Act Section 7(a)(2) Biological and Conference Opinion, and Magnuson- Stevens Fishery Conservation and Management Act Essential Fish Habitat Response for the California High Speed Rail Merced to Fresno Section, including the Central Valley Wye NMFS Consultation Number: WCR-2018-10897/WCRO-2018-00285 Action Agency: California High Speed Rail Authority Affected Species and NMFS’ Determinations: ESA-Listed Species Status Is Action Likely Is Action Is Action Likely Is Action Likely to Adversely Likely To to Adversely To Destroy or Affect Species? Jeopardize Affect Critical Adversely Modify the Species? Habitat? Critical Habitat? California Central Threatened Yes No N/A1 N/A Valley steelhead (Oncorhynchus mykiss) distinct population segment (DPS) Central Valley Threatened N/A2 No N/A1 N/A spring-run Chinook salmon (O. tshawytscha), Non- essential experimental population Fishery Management Plan That Does Action Have an Adverse Effect Are EFH Conservation Identifies Essential Fish Habitat in on EFH? Recommendations Provided? the Project Area Pacific Coast Salmon Yes Yes Consultation Conducted By: National Marine Fisheries Service, West Coast Region Date: September 3, 2019 1 California Central Valley steelhead and Central Valley spring-run Chinook salmon critical habitats do not occur within the action area. 2 Within the action area, non-essential experimental population Central Valley spring-run Chinook salmon are governed by a final rule under Endangered Species Act Section 10(j) and only a jeopardy determination can be made regarding a project’s impact on the population. While take of this population is exempt from Section 9 prohibitions within the action area, the California High Speed Rail Authority has agreed to treat this population as a threatened species and receive this conferencing opinion to minimize or avoid impacting this population. Table of Contents TABLE OF CONTENTS TABLE OF CONTENTS ................................................................................................................ ii LIST OF TABLES ......................................................................................................................... iv LIST OF FIGURES .........................................................................................................................v LIST OF ACRONYMS ................................................................................................................. vi 1. INTRODUCTION ..................................................................................................................1 1.1 Background ......................................................................................................................... 1 1.2 Consultation History ........................................................................................................... 1 1.3 Proposed Federal Action ........................................................................................................... 4 2. ENDANGERED SPECIES ACT: .......................................................................................14 2.1 Analytical Approach ......................................................................................................... 14 2.1.1 Conservation Banking and ILF Participation in the Context of the ESA Environmental Baseline ............................................................................................................................. 15 2.2 Rangewide Status of the Species and Critical Habitat ...................................................... 16 2.2.1 CCV steelhead DPS status ................................................................................................... 17 2.2.2 NEP CV spring-run Chinook salmon status ........................................................................ 18 2.2.3 Climate change..................................................................................................................... 20 2.3 Action Area ....................................................................................................................... 22 2.4 Environmental Baseline .................................................................................................... 27 2.4.1 Occurrence of listed species................................................................................................. 27 2.4.2 Factors affecting listed species ............................................................................................ 32 2.4.3 Conservation and restoration efforts .................................................................................... 40 2.5 Effects of the Action ......................................................................................................... 42 2.5.1 Direct and indirect effects to species ................................................................................... 42 2.5.2 Interrelated and interdependent action effects to species .................................................... 64 2.5.3 Interrelated and interdependent action effects to designated critical habitat ....................... 67 2.6 Cumulative Effects............................................................................................................ 68 2.7 Integration and Synthesis .................................................................................................. 70 2.8 Conclusion ........................................................................................................................ 72 2.9 Incidental Take Statement................................................................................................
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