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Final Biological Opinion Concerning the Operation of the Missouri River

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Final Biological Opinion Concerning the Operation of the Missouri River United States Department of the Interior FISH AND WILDLIFE SERVICE Mountain-Prairie Region IN REPLY REFER TO: rWS/R6/ MAILING ADDRESS: STREET LOCATION: Post Office Box 25486 134 Union Boulevard TAILS Ref: Denver Federal Center Lakewood, Colorado 80228-1807 06E00000-2018-F-O Denver, Colorado 80225-0486 APR 1 3 2018 Mr. David J. Ponganis Director of Programs Directorate U.S. Army Corps of Engineers, Northwest Division P.O. Box 2870 Portland, Oregon 97208~2870 Oc~ve,.- Dear.... Mr . ..Ponga ms: Please find enclosed the Final Biological Opinion concerning the Operation of the Missouri River Mainstem Reservoir System, the Operation and Maintenance of the Bank Stabilization and Navigation Project, the Operation of Kansas River Reservoir System, and the Implementation of the Missouri River Recovery Management Plan. The U.S. Fish and Wildlife Service (Service) transmitted the draft to the USACE on February 8, 2018 and the USACE subsequently transmitted the draft BiOp to the Independent Science Advisory Panel (ISAP) of the Missouri River Recovery Implementation Committee (MRRIC). The ISAP presented the results of their review to the MRRIC plenary session March 27, 2018 and the USACE formally transmitted the ISAP response along with USACE supporting information to the Service on April 3, 2018. The Service wants to thank the lJSACE for their continued collaborative approach to what is a ground breaking process of evaluating a highly complex adaptive management process through section 7 of the Endangered Species Act. The Service has taken the ISAP and USACE comments under advisement and have made numerous improvements to the document as a result. As you are aware the draft IliOp did not have a fully developed Incidental Take Statement (ITS). The Service provided concept papers to the USACE and MRRIC at the MRRIC plenary session mentioned above. While there was not an explicit charge to the ISAP to review and comment on the ITS both the USACE and the Service received review comments on the ITS on April 4, 2018. In summary the ISAP expressed concern over using survival of pallid sturgeon as the metric for the ITS, particularly in the lower river. Service and USACE staff have been working very closely on addressing ISAP concerns. The Service also continued to engage our fisheries professionals on how to address the ISAP concerns. At the end of the day the Service has concluded to continue to utilize survival estimates of pallid sturgeon as a metric in both the upper and lower Missouri River. However, in light of the ISAP comments the Service has developed a second metric in the lower Missouri river that relies on catch per unit effort as was suggested by the ISAP. Further explanation of the rationale can be found in the Final BiOp. The Service anticipates that as a result of monitoring and evaluation through the adaptive management process refinements to one or both of those metrics is likely. 2 There remains two process documents that will need to be completed prior to completion of the Record of Decision. The first is a process and procedures document that will describe how subsequent step down consultations will be addressed in the future. The second is a process mechanism for the Service to provide to the USACE a periodic progress review regarding overall implementation of the Final Bi Op. Both our staffs are aware of these and will be turning to develop those shortly. In closing, I would like to thank you and USACE staff for working so closely with the Service on developing a very complex and cutting edge program to further conservation of threatened and endangered species within the Missouri River Basin. The Service firmly believes that this approach will improve conditions for protected species through time while ensuring the USACE's ability to meet the authorized purposes on the Missouri River and allowing better opportunities to address human considerations throughout the basin. If you have any questions please feel free to contact me at 303-236-4210 or Ms. Kimberly Smith at 303-236-434 7. Sincerely, Assistant" Regional Director... - ~Ecological Services Enclosure: Final Biological Opinion concerning the Operation of the Missouri River Mainstem Reservoir System, the Operation and Maintenance of the Bank Stabilization and Navigation Project, the Operation of Kansas River Reservoir System, and the Implementation of the Missouri River Recovery Management Plan Cc: U.S. Fish and Wildlife Service, Regional Director - Region 6 U.S. Fish and Wildlife Service, Regional Director - Region 3 Rocky Mountain Regional Office, Office of the Solicitor - Attn: Lori Caramanian BIOLOGICAL OPINION Operation of the Missouri River Mainstem Reservoir System, the Operation and Maintenance of the Bank Stabilization and Navigation Project, the Operation of Kansas River Reservoir System, and the Implementation of the Missouri River Recovery Management Plan TAILS No. 06E00000-2018-F-0001 FISH AND WILDLIFE SERVICE Mountain Pra.irie Region Denver, Colorado ., ,1 ,~ Assistant Regional Director for Ecological Services _ _:_ __,~'":::: ====~''~~~~--'...:.::,~""ssL:::::....__ Date ~--~ April 13, 2018 EXECUTIVE SUMMARY This biological opinion (BiOp) is issued in response to the U.S. Army Corps of Engineers’ (USACE) request for initiation of section 7 consultation on October 30, 2017. This BiOp supersedes the 2003 Amended BiOp and associated ITS dated December 16, 2003, which addressed the effects of Operation of the Missouri River Mainstem Reservoir System, Operation and Maintenance of the Missouri River Bank Stabilization and Navigation Project, Operation of the Kansas River Reservoir System. The USACE has described its proposed changes to the Project and the effects of these changes in the revised amended BA dated October 30, 2017 and in their letter dated January 19, 2018. Where appropriate, we have incorporated its descriptions and analysis into this BiOp. The Proposed Action that we are evaluating in this BiOp is the Operation of the Missouri River Mainstem Reservoir System, the Operation and Maintenance of the Bank Stabilization and Navigation Project, the Operation of Kansas River Reservoir System, and the Implementation of the Missouri River Recovery Management Plan. The Science and Adaptive Management Plan, a component of the Proposed Action, describes the formal process led by Service and USACE in implementing the Missouri River Recovery Management Program. The U.S. Fish and Wildlife Service (Service) has been consulting with the USACE on Missouri River Mainstem Reservoir System operations since 1986 following the listing of the interior least tern (Sternula antillarum) and piping plover (Charadrius melodus) under Endangered Species Act (ESA or Act). Although consultation activities began with the Missouri River System operations, they expanded to include Bank Stabilization and Navigation Project (BSNP) operations and maintenance and Kansas River reservoir operations within the scope of the Proposed Action and also included evaluation of effects to pallid sturgeon (Scaphirhynchus albus) following its ESA listing in 1990. Consultation activities occurring through 2003 are described in detail in the 2000 BiOp (Service 2000) and 2003 Amended BiOp (Service 2003). The 2003 Amended BiOp included a jeopardy opinion with a Reasonable and Prudent Alternative for pallid sturgeon and a non-jeopardy opinion for interior least tern and piping plover. The 2003 Amended BiOp also called for development of a framework for resource management actions on the Missouri River, acknowledging critical uncertainties about how the species will respond to implemented management actions. In 2005, USACE established the Missouri River Recovery Program (MRRP). It is the umbrella program that coordinates the USACE efforts in the following: • Compliance with the 2003 Amended BiOp on the Operation of the Missouri River Mainstem Reservoir System, Operation and Maintenance of the BSNP, and Operation of the Kansas River Reservoir System; • Acquiring and developing lands to mitigate for lost habitats as authorized in Section 601(a) of WRDA 1986 and modified by Section 334(a) of WRDA 1999 (collectively known as the BSNP Fish and Wildlife Mitigation Project); and • Implementation of WRDA 2007 including the Missouri River Recovery Implementation Committee (MRRIC) and Section 3176, which allowed USACE to use recovery and mitigation funds in the upper basin states of Montana, Nebraska, North Dakota, and South Dakota. EXECUTIVE SUMMARY 1 April 13, 2018 The MRRIC makes recommendations and provides guidance to federal agencies on the existing MRRP. The MRRIC is composed of over 70 members representing various interests, Tribes, states, and agencies from within the Missouri River basin. In 2011, the MRRIC and USACE established the Independent Science Advisory Panel (ISAP). This panel is charged with independent science support and technical oversight by providing advice on specific topics. Doyle et al. (2011) identified the need for the MRRP to incorporate new scientific information that has become available since the issuance of the 2003 Amended BiOp. An Effects Analysis study, recommended by Murphy and Weiland (2011), was initiated in 2013 to synthesize new scientific information specific to these three species and concluded that considerable uncertainty remains regarding the type and extent of management actions ultimately needed to lead to population growth for each of the three species. Given the high level of uncertainty regarding the necessary actions to address the listed species’ needs,
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