2014 AFS Cal-Neva 48th Annual Conference Program

California-Nevada Chapter of the American Fisheries Society
48TH ANNUAL CONFERENCE MARCH 27 29, 2014
Embassy Suites Sacramento Riverfront Promenade

100 CAPITOL MALL, SACRAMENTO CA 95814
Table of Contents
Schedule in Brief Conference Theme Acknowledgments General Information Plenary Speakers Thursday Afternoon Sessions
Continuing Education Hatchery Forum
2 3 4 6-7 8-11 12-14 12 14 15 16-21 16 17 18 19-20 21 22-25 22 23-24 25 26 -28 26 27 28 29-65 66-75
Friday Morning Welcome & Plenary Session Friday Afternoon Technical Sessions
Hydroacoustic Symposium Dam Removal and Water Quality Challenges, Collaboration, and Solutions in FERC Relicensing Stream Management and Restoration in California Collaborating for the Future Science Informing Green Sturgeon Restoration
Saturday Morning Technical Sessions

Acoustic Telemetry Can we link salmonid biology with freshwater habitat for successful restoration? Native Fishes
Saturday Afternoon Technical Sessions

General Symposium San Joaquin River Restoration Program Fish Genetics
Oral Presentation Abstracts Poster Presentation Abstracts
CAL-NEVA 48TH ANNUAL CONFERENCE.
Schedule in Brief
Thursday, March 27, 2014
Registration Hatchery Forum
1:00pm 6:00pm 8:00am 5:00pm Atrium
Poster Set-up
8:30am 5:00pm Terrace
Poster Session - Welcome Social, Job Fair, and Vendor Show

6:00pm 9:00pm Atrium and Terrace
Vendor Set-up and Display

8:30am 5:00pm Atrium and Terrace
Student Social (everyone is welcome)

9:00pm 12:00am Joe's Crab Shack
Continuing Education Sessions

8:30am 5:00pm
Friday, March 28, 2014

Registration
8:00am 5:00pm Atrium
Chapter Business Lunch Meeting

12:00pm 1:00pm Rio City Cafe
Welcome & Plenary Session: Challenges. Collaboration. Solutions.

8:30am 12:00pm Old Sacramento Ballroom
Technical Sessions
1:00pm 5:00pm
Student-Mentor Lunch I
12:00pm 1:00pm Atrium
Banquet
7:00pm 12:00am Old Sacramento Ballroom
Saturday, March 29, 2014

Spawning Run Registration
6:20am 7:30am Behind Tower Bridge Bistro by the riverfront
Student-Mentor Lunch II
12:00pm 1:00pm Downtown Sacramento
8:00am 10:00am Atrium
Afternoon Technical Sessions

1:00pm 5:00pm
Morning Technical Sessions

8:00am 12:00pm
CHALLENGES. COLLABORATION. SOLUTIONS.
Challenges. Collaboration. Solutions.
Conference Theme
The theme for the 48th Annual Conference of the American Fisheries Societys California-Nevada Chapter (Chapter) is Challenges. Collaboration. Solutions. This conference will address the type of fisheries professionals needed and the relevance of partnerships to tackle present and future environmental threats to our fishes and their aquatic ecosystem that affect fishery resources in California and Nevada. The plenary speakers for this conference were carefully selected to represent different areas of expertise, knowledge, and influence in both fisheries science and regulatory policies. They will talk about their role as leaders to improve the conservation and sustainability of fishery resources; Four Continuing Education Courses are being offered that cover genetics and regulatory processes for both state and federal policies. These courses are offered at a highly discounted price for professionals and free to our student members. A hatchery forum is also offered to discuss the science and management of hatchery and natural origin of salmonids in the Central Valley; and This year's technical sessions are arranged to showcase our scientists' different areas of expertise and knowledge in both fisheries and environmental sciences and regulatory policies. These technical sessions are as follows: native fishes, fish genetics, dam removal, large scale restoration projects, stream management, sturgeon, telemetry, FERC, and hydroacoustics.
Acknowledgements
AFS Cal-Neva Planning Committee
Planning Committee Chair Program Development Trade Show Continuing Education Conference Logo Catering Time and Place Local Arrangements Fundraising Student Presentation/Poster Judging Registration Raffle Spawning Run Poster Session Signage and Job Fair Audio/Video and Computers Student Volunteer Organizer Budget Merchandise Student-Mentor Luncheon Photographer Norm Ponferrada Myfanwy Johnston Felipe La Luz Michael Carbiener Claire Stouthamer Ingel Laurie Earley Mary Nicholl Eva Bush Tom Keegan Sharon Shiba Russell Barabe Jasmine Shen Kirsten Sellheim Jon Cook Felipe La Luz Alan Noble Webster Gena Lasko Christina Parker Brian Williamson Ivan Parr Research Assistant Biologist University of California, Davis URS Corporation Fisheries and Wildlife Biologist Graduate Student Research Assistant Senior Fisheries Biologist Environmental Scientist Fish Biologist Research Permits Research Assistant Senior Fisheries Scientist Senior Biologist Specialist Environmental Scientist Scientific Aid Fishery Biologist Research Assistant Research Assistant Student Environmental Scientist AFS Cal-Neva President-elect University of California, Davis University of California, Davis URS Corporation California Department of Fish and Wildlife US Fish and Wildlife Service NOAA Fisheries University of California, Davis AECOM California Department of Fish and Wildlife California Department of Fish and Wildlife California Department of Water Resources Cramer Fish Sciences University of California Davis University of California, Davis University of California, Davis California Department of Fish and Wildlife
Acknowledgements
General Information
Registration
General Information
Onsite registration will be available in the Atrium on Thursday, March 27th and Friday, March 28th from 8:00am 5:00pm, and Saturday, March 29th from 8:00am 10:00am. Pre-registered attendees can pick up conference materials here.
Banquet
The Banquet will be held in the Old Sacramento Ballroom on Friday, March 28th from 7:00pm 12:00am.
Social Hour
The student social will occur on Thursday, March 27th from 9:00pm until 12:00am at Joe's Crab Shack in historic Old Sacramento, just across the street from the Embassy Suites. Joe's Crab Shack offers a variety of dishes from land to sea as well as salads for those so inclined. Joe's Crab Shack also offers a full bar. This is a great time to informally commingle with colleagues and other professionals. Everyone is welcome to come and hang out. Joe's Crab Shack can accommodate all of us!
Commercial Exhibits
Commercial exhibits will be on display in the Atrium. Vendor setup and display will take place on Thursday, March 27th from 8:30am 5:00pm.
Student Job Fair Student-Mentor Lunch
The Job Fair will be held in the Terrace on Thursday, March 27 from 6:00pm 9:00pm.
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You must be fully registered to sign up. There will be two lunch opportunities: (1) Friday, March 28, 2014 during lunch hour or (2) Saturday, March 29, 2014 at noon following the conclusion of the meeting at a restaurant of the mentors choosing.
Student Paper and Poster Competition

Student papers and posters will be in the running for cash prize awards. All posters will be judged Thursday evening during the poster session.
Annual Business Meeting

The AFS Cal-Neva Chapter Annual Business Meeting will begin at 12:00pm 1:00pm on Friday, March 28th at Rio City Cafe across the street from the Embassy Suites.
Spawning Run
5K Spawning Run will begin at Discovery Park and continue alongside the beautiful American River. This route is completely paved and mostly shaded by the lush riparian habitat surrounding the river. During the run, you may also get lucky and catch glimpses of various unsuspecting wildlife. Join us on March 29, 2014 at 6:00am.
Plenary Speakers
Stephanie Carlson, Ph.D.
ASSISTANT PROFESSOR OF FRESHWATER FISH ECOLOGY UNIVERSITY OF CALIFORNIA AT BERKELEY Stephanie received her B.S. from UC Davis, a Masters from UMass Amherst, and her PhD from the School of Aquatic & Fishery Sciences at the University of Washington. She started as faculty at Berkeley in 2008 where she teaches classes on Fish Ecology and Freshwater Ecology. Since starting this position, she has worked to grow interest in fish and aquatic ecology at Berkeley and beyond. Her primary research interest is in understanding the dynamics of freshwater fish populations, particularly the factors that shape these populations and influence their persistence.
Collaboration and multidisciplinary science: reflections from a junior faculty member

Stephanie Carlson, Environmental Science, Policy & Management 130 Mulford Hall #3114, UC Berkeley, Berkeley, CA 94720 (510) 643-9704, smcarlson@berkeley.edu
It is broadly recognized that some of our most challenging environmental problems can only be addressed through multidisciplinary science, and yet most of our training continues to be strongly disciplinary. In this talk, Ill discuss my own transition from graduate student to faculty member, and some of the challenges I have faced as my network of collaborators has grown to include researchers outside of my discipline and agency scientists. Ill discuss some of the lessons that Ive learned, the most important being the need to provide our students with both specialized and interdisciplinary training. In so doing, we can help educate the next generation of problem solvers and impart skills that may translate into creative solutions to real-world problems.
Christina (Tina) Swanson, Ph.D.

DIRECTOR, SCIENCE CENTER NATIONAL RESOURCES DEFENSE COUNCIL (NRDC) Tina works to expand the organizations scientific capabilities and support its legal and policy work across a range of environmental, public health and sustainable management issues. Prior to joining NRDC in 2011, Dr. Swanson worked with The Bay Institute (Novato, CA), serving as the organizations fisheries/senior scientist and, from 2008-2011, as Executive Director and Chief Scientist. She is an expert in fish biology, aquatic ecosystem protection and restoration, ecological indicators and water resource management. Much of her work has been in the San Francisco Bay-Delta, but she has also worked and conducted research on marine and estuarine fish in Hawaii and, as a Fulbright Scholar, in the Philippines. Dr. Swanson has authored or co-authored more than 20 peer-reviewed articles and numerous technical and policy memoranda and reports. Dr. Swanson received her B.A. from Cornell University, her
doctorate from University of California, Los Angeles, and conducted post-doctoral research at University of California, Davis. She was President of the Western Division of the American Fisheries Society in 2012-2013 and of the California-Nevada Chapter in 2004-2005.
Plenary Speakers
Challenging Times in the Bay-Delta: Rules and Tools for Getting Collaborators on the Same Page
Christina Swanson, Natural Resources Defense Council 111 Sutter Street, 20th Floor, San Francisco, CA 94104 (415) 875-6100, cswanson@nrdc.org
The most important scientific endeavors and the most effective and durable science-based policy agreements are almost always the product of collaboration. But collaboration only works if everyone agrees on the ground rules. The challenge of developing a science-based plan for ecosystem protection and management for the San Francisco Bay-Delta seems a case in point: the parties not only disagree on the identity and significance of environmental drivers of ecosystem condition but also on what constitutes sound, credible, useful science. One approach to overcoming this conflict is use of carefully designed decision support tools, such as the one developed by the CALFED Bay-Delta Programs Adaptive Management Planning Team (AMPT) and the Delta Regional Ecosystem Restoration Implementation Plan (DRERIP). The DRERIP toolkit includes a collection of consistently structured and linked conceptual models of Delta species life histories, habitats, ecosystem processes, and the physical, chemical and biological stressors that affect those processes; a comprehensive quantitative description of physical and chemical existing conditions; specific guidance for describing proposed ecosystem restoration actions; a structured evaluation process designed to consider the worth, risk, reversibility and opportunities to learn for each proposed restoration or management action; and a decision tree to determine which proposed actions merit implementation or additional research. DRERIP was itself a collaboration of academic, agency, and stakeholder scientists. Building upon its work and using its structured approach, which provides rules and tools for effective and productive collaboration, could improve both process and outcomes for our current challenges in the west coasts largest estuary.
David J. Manning, M.S.

ENVIRONMENTAL RESOURCES COORDINATOR SONOMA COUNTY WATER AGENCY David earned an M.S. in Fisheries from Humboldt State University and B.S. in Natural Resources from UC Berkeley. He has worked for the Sonoma County Water Agency for the past 15 years. As an Environmental Resources Coordinator, he manages teams of scientists and planners dedicated to minimizing the effects of water supply, flood control, and sanitation activities on threatened and endangered steelhead, Chinook salmon, and coho salmon. Before joining the Water Agency in 1999, he was a fishery biologist for the National Park Service at Point Reyes National Seashore and Golden Gate National Recreation Area. He is Past-President of the California-Nevada Chapter of the American Fisheries Society and served as Associate Editor for the North American Journal of Fisheries Management.
Were with the government and were here to help a tale of challenges, collaborations, and solutions for enhancing salmon and steelhead habitat in Wine Country
CAL-NEVA 48TH ANNUAL CONFERENCE. 9
Plenary Speakers
David Manning, Sonoma County Water Agency 404 Aviation Blvd. Santa Rosa, CA 95403 (707) 547-1988, David.Manning@scwa.ca.gov
To provide water supply and flood control for 600,000 residents, the Sonoma County Water Agency and U.S. Army Corps of Engineers regulate flow from Warm Springs Dam/Lake Sonoma along 23 km of Dry Creek, a major Russian River tributary. Bordered by nearly 200 private properties, Dry Creek flows through a highly valuable grape growing region. To improve stream flow and habitat conditions for coho and steelhead, the National Marine Fisheries Service issued a 15 year Biological Opinion in September 2008 that mandates large scale enhancement of 11.5 km of Dry Creek summer and winter rearing habitat. Guided by an adaptive management and monitoring plan, enhancement work is designed in phases. Construction of the first phase commenced in 2012 and will be completed in 2014. This presentation focuses on the Sonoma County Water Agencys experience working collaboratively with a variety of stakeholders including private property owners, state and federal agencies, and water customers. I will provide insights on approaches that we found most helpful in a system with considerable technical and institutional challenges. Major challenges included different opinions on what constitutes risk or benefit to property owners, methods to acquire needed property rights, approaches to defining project success, habitat enhancement techniques, and appropriate scales and types of monitoring.
Jeffrey McLain, M.S.

DIVISION MANAGER, NATIONAL MARINE FISHERIES SERVICE CALIFORNIA CENTRAL VALLEY AREA OFFICE Jeff is the California Central Valley Division Manager for the National Marine Fisheries Service and works with federal and state agencies to implement the Endangered Species Act. Jeff has also worked for the U.S. Fish and Wildlife Service as the San Joaquin River Restoration Program Coordinator as part of the multi-agency office with the U.S. Bureau of Reclamation, as a Habitat Restoration Coordinator for the Central Valley Project Improvement Act Anadromous Fish Restoration Program, and for the Juvenile Fish Monitoring Program as part of the Interagency Ecological Program. He was the CaliforniaNevada Chapter President in 2007.
Collaborating in the California agency melting pot: coping and solutions

Jeffrey McLain, National Marine Fisheries Service California Central Valley Area Office, 650 Capitol Mall, Suite 5-100, Sacramento, CA 95814, (916) 930-5647, Jeff.McLain@noaa.gov
The fisheries practitioner in California will spend considerable time working with a myriad of federal and state agencies, academic institutions, and nonprofits and private firms. The cultures of these many organizations are very different and must be navigated. How does one collaborate in such an environment? The author will discuss the role of agency culture in collaborations, share firsthand experiences, and offer some best practices for consideration.
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Plenary Speakers
Bradley Cavallo, M.S.
SENIOR SCIENTIST CRAMER FISH SCIENCES Brad earned a M.S. in Aquatic Ecology from University of Montana and a B.S. in Fisheries from UC Davis. Since joining Cramer Fish Sciences in 2006, Brad has led a growing team of consulting scientists working to help resolve some of Californias most vexing fisheries management challenges. His project experiences range from evaluating and planning anadromous hatchery programs to developing simulation models to represent the influence of water project operations and habitat quality on juvenile salmon and steelhead. Brad began his professional career in 1997 with the California Department of Fish and Wildlife and worked for California Department of Water Resources from1999 through 2006. Brad is currently President of Cramer Fish Sciences and is a Past-President of the CaliforniaNevada Chapter of the American Fisheries Society.
In the dance between science and policy, who leads?

Brad Cavallo, Cramer Fish Sciences 1300 New Airport Rd. STE 102 Auburn, CA 95602 (530) 888-1443 x11, bcavallo@fishsciences.net
With many California fishes threatened and resource conflicts seemingly intensifying, managers and policy makers have proclaimed their embrace of collaborative science. But what is collaborative science and how is it accomplished? One approach emphasizes a top-down process, wherein managers and sometimes attorneys establish a "policy team which carefully selects participants and identifies topics they judge appropriate for technical discussion. Another approach identifies problems and objectives and then allows a diverse group of scientists to weigh evidence for which approaches are most likely to contribute to achieving fish population objectives. Collaborative science for Central Valley salmonids to date has largely followed the former, and rarely embraced the latter. If we wish to advance recovery of threatened fish, problem-solving science needs to be favored over policy-constrained science. University and consulting scientists, being less encumbered by existing policy directives and from judgments of policy makers, may be uniquely valuable to collaborative science efforts. However, to make substantial progress in species recovery, fisheries scientists of all affiliations require freedom to explore creative, evidence-supported solutions without perceived or real constraints from policy decision makers.
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Continuing Education
Introduction to Genetics Monitoring

9:00am 5:00pm Steamboat Instructors: Scott Blankenship, Ph.D.1,2, and Gregg Schumer1,2
1 2
Cramer Fish Sciences, GENIDAQS Division, West Sacramento, CA (www.fishsciences.net) UC Davis, College of Agriculture and Environmental Sciences, Davis, CA.
Despite considerable investment of time and resources, information outcomes from monitoring programs can be substandard or unnecessarily limited in utility. Rapid technical advancements in population genetics and molecular biology are providing many novel, relatively low cost techniques and technologies that are applicable and powerful tools for fisheries biologists. These technical advancements can be applied within current monitoring/recovery programs to vastly improve the informed management of fishes. This course will be presented in two sections. The first section will include a non-technical primer on how genetic information is obtained and examples of molecular diagnostic tool applications. The second section will focus on population level ( e.g., mixture analysis) and individual level (e.g., molecular tagging) methods. Objectives: o To bridge the divide between rapid technical advancements and their use in resource management and field ecology. o To introduce basic genetics terminology and processes. o To introduce genetics-based monitoring techniques. o To provide attendees with a working knowledge of molecular diagnostic techniques. o To provide attendees with a working knowledge of population level and individual-based monitoring methods. We encourage group discussion throughout the course. Questions and comments are welcome within the workshop framework. Additionally, we welcome constructive evaluations, suggestions, and comments regarding the course. This workshop is intended for non-geneticists to gain a basic understanding of new monitoring techniques and how they may be applied. This will not be a difficult course, and there will be no grades. Yet, individuals that actively listen, strive to apply course concepts to areas of personal interest, and participate in group activities and discussion will get the most out of this course.
Introduction to CEQA
8:00am 12:00pm Schoolhouse Instructor: Geoff Thornton, URS Corporation, Senior Environmental Planner
This course will discuss and describe the California Environmental Quality Act (CEQA). Discussion topics will include a brief history of CEQA, the intent and purposes of CEQA, and an overview of the process of CEQA compliance.
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Continuing Education
Section 7 Consultation
8:00am 12:00pm Central Pacific Instructor: Rob Nielsen PhD, NOAA Fisheries, Section 7 Coordinator
NOAA's National Marine Fisheries Service (NMFS) will lead this workshop informing Federal agency, applicant, and consulting biologists on the types of section 7 consultations under the Endangered Species Act (ESA) for project effects to federally listed anadromous fishes. NMFS will provide an overview of the ESA Section 7 and the Magnuson-Stevens Fishery Conservation and Management Act (MSA) essential fish habitat (EFH) consultation processes, including a description and checklist of the necessary information required in a biological assessment (BA) to initiate section 7 consultation for a project action with a Federal nexus.
Section 10 and 4(d) Rule

1:00pm 5:00pm Central Pacific Instructors: Mary Nicholl, Ocean Associates, Fisheries Biologist; Amanda Cranford, Ocean Associates, Fisheries Biologist; and Jeffrey Jahn, NOAA Fisheries, Supervisor
The National Marine Fisheries Service will lead this workshop informing researchers on the types of take covered under the Endangered Species Act (ESA) for research and monitoring activities on ESA-listed anadromous fishes. NMFS will provide an overview the ESA Section 10(a)(1)(A) permit or 4(d) research approval processes including a demonstration of how these permits can be applied to the NMFS Authorizations and Permits for Protected Species (APPS) Website at https://apps.nmfs.noaa.gov.
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Hatchery Forum
Can we have our salmon and eat them too? A forum for discussing the science and management of hatchery and natural origin salmonids in the Central Valley
1:00pm 6:00pm Schoolhouse Moderators: Bradley Cavallo, Cramer Fish Sciences, Principal Scientist and Matt Nobriga, USFWS, Fisheries Biologist
The forum has two interrelated objectives: 1. Provide knowledgeable scientists an opportunity to share the latest information regarding the degree to which hatchery salmon and steelhead may be influencing the conservation status of Central Valley salmonids stocks; in particular steelhead, fall Chinook and spring Chinook. 2. Provide an opportunity for a panel of knowledgeable scientists, managers, and stakeholders to discuss and debate best available science and implications for related management actions. Speakers and Panelists: Carlos Garza (NMFS Southwest Fisheries Science Center), Stephanie Carlson (University of California, Berkeley), Rachel Johnson (Cramer Fish Sciences & University of California Davis), Scott Hamelberg (US Fish and Wildlife Service), Brad Cavallo (Cramer Fish Sciences), Kevin Shaffer (California Department of Fish and Wildlife), Brett Kormos (California Department of Fish and Wildlife), JD Wikert (US Fish and Wildlife Service), Dick Pool (Golden Gate Salmon Association). Presentation Topics: Status of hatchery and natural-origin Central Valley anadromous salmonids Scientific implications (for ecology, fitness and conservation) from hatchery/natural origin patterns observed in Central Valley Discussion of likely outcomes from management alternatives (including the no-action alternative) which attempt to address hatchery related effects. This would also call out actions identified in the CA HSRG or not identified in the CA HSRG. Expected Attendees: biologists, managers, media, public, Hatchery Conservation Team members Desired Outcome: Attendees fully updated on status of Central Valley hatchery salmon, steelhead and related implications for conservation and recovery of natural origin and ESA listed stocks. The entire proceeding would be recorded and made available online for others to review. Paper to be submitted to the journal Fisheries.
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Morning Plenary Session

Welcome & Plenary Session: Challenges. Collaboration. Solutions.

8:30am 12:00pm Old Sacramento Ballroom Moderator: Norm Ponferrada
Time
8:30am 8:45am
Speaker
Patrick Crain
Presidents announcement
8:45am 9:00am
Norm Ponferrada
President-elects introduction
9:00am 9:20am
Stephanie Carlson
Collaboration and multidisciplinary science: reflections from a junior faculty member
9:20am 9:40am
Tina Swanson
Challenging times in the Bay-Delta: rules and tools for getting collaborators on the same page
9:40am 10:00am
David Manning
Were from the government and were here to help a tale of challenges, collaborations, and solutions for enhancing salmon and steelhead habitat in Wine Country
10:00am 10:30am 10:30am 10:50am
BREAK Jeff McLain
Collaborating in the California agency melting pot: coping and solutions
10:50am 11:10am
Bradley Cavallo
In the dance between science and policy, who leads?
11:10am 12:00am
PANEL DISCUSSION
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Session I: Hydroacoustic Symposium

1:00pm 3:00pm Steamboat Moderator: Cynthia LeDoux-Bloom, Senior Marine Scientist, AECOM and ManTech International
Effects of anthropogenic noise on fishes: hydroacoustic fundamentals, regulatory criteria, and physio-behavioral concerns
There is increasing world-wide concern that the anthropogenic noise produced by aquatic activities such as construction, water export, wave energy, vessel traffic, and military exercises have the potential to negatively affect fishes. Noise produced by pile-driving, water pumping, tidal turbines, boat engines, and seismic air-guns blasts result in varying degrees of physio-behavioral changes that may affect the survival of individual fish, populations, or species. Barotrauma can occur during rapid changes in pressure that affect the internal gas equilibrium in fish. The swim bladder, blood, and other tissues may expand or contract in reaction to rapid pressure changes resulting in tissue damage, organ failure, mortality and/or emigration from the source noise. Under both the United States Endangered Species Act (ESA) and the Magnuson-Stevens Fishery Conservation and Management Act, agencies are required to consult with NOAA Fisheries if any action they are taking will adversely affect any of the listed species or Essential Fish Habitat. The U.S. West Coast is home to many ESA-listed anadromous, migratory fishes such as several salmonid species and green sturgeon. Developing regulatory criteria, industry standards, and cooperative research across multiple jurisdictional waters creates enormous challenges which require committed collaboration to develop creative solutions. The goal of this session is to present hydroacoustic fundamentals, current regulations, criteria applied to industry standards, and the most recent research on the effects of pile driving, tidal turbines, and boat noise on the physiobehavior of fishes.
Time
1:00pm 1:20pm 1:20pm 1:40pm 1:40pm 2:00pm 2:00pm 2:20pm 2:20pm 2:40pm 2:40pm 3:00pm
Speaker
James Reyff
Underwater anthropogenic sound that may harm fish: Fundamentals, monitoring and control
Jacqueline Pearson-Meyer Melinda Molnar

Christa Woodley Tye Nichols
Assessing the effects on fishes from pile driving sound: Application of hydroacoustic criteria Pile driving on large bridge projects in CA; Case studies of aquatic species impacts and attenuation methodology Effects of short-term tidal turbine exposure on fish hearing and tissues Physiological effects of boat noise on a coastal marine fish, the giant kelpfish (Heterostichus rostratus)
Sarika Cullis-Suzuki
Effects of boat noise on a wild, vocal fish, plainfin midshipman ( Porichthys notatus)
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Session II: Dam Removal and Water Quality

3:20pm 5:00pm Steamboat Moderator: Michael Carbiener, Senior Fisheries Biologist, URS Corporation
Time
3:00pm 3:20pm 3:20pm 3:40pm 3:40pm 4:00pm
Speaker
BREAK Shawn Chartrand
Perspectives on design of step-pool stream channel segments
Michelle Workman
Successes from a low head dam removal project on an ephemeral Mokelumne River tributary in the Central Valley of California
4:00pm 4:20pm 4:20pm 4:40pm
Chris Hammersmark Stephen Louie
Branciforte dam removal project, Branciforte Creek, Santa Cruz, California Important factors influencing predatory fish mercury concentrations in California reservoirs: A statistical approach
4:40pm 5:00pm
Carrie Austin
Reservoir management strategies to reduce fish mercury levels: an integral part of the statewide reservoir mercury TMDL
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Sessions I & II: Challenges, Collaboration, and Solutions in FERC Relicensing

1:00pm 5:00pm Tower Bridge Moderator: Scott Wilcox, Principal/Senior Fisheries Biologist, Stillwater Sciences
Time
1:00pm 1:20pm 1:20pm 1:40pm
Speaker
Scott Wilcox
Challenges, collaboration, and solutions in the FERC relicensing process.
Catalina E. Reyes
Collaborative efforts to provide cool water for holding spring-run Chinook Salmon (Oncorhynchus tshawytscha) in Butte Creek, Butte County, CA.
1:40pm 2:00pm
Sarah Kupferberg
Declining downstream: Modeling efforts to assess recruitment to frog populations in California's regulated rivers.
2:00pm 2:20pm
Ryan Peek
Plasticity of breeding in Foothill Yellow-legged Frog (Rana boylii) in the Sierra Nevada: Best Monitoring Practices
2:20pm 2:40pm 2:40pm 3:00pm
Sarah Yarnell
Management of the spring snowmelt recession in regulated systems
Jarvis Caldwell
Data overload: Interfacing with new graphical tools for handling a data rich environment
3:00pm 3:20pm 3:20pm 3:40pm
BREAK Greg Pasternack

Use of near-census river science to avoid conflicts in FERC Relicensing due to statistical sampling ambiguity
3:40pm 4:00pm
Elizabeth A. Campbell
Yuba River Development Project FERC Integrated Licensing process: U.S. Fish and Wildlife Service perspective
4:00pm 4:20pm 4:20pm 5:00pm
Curtis Knight
Klamath River: out of the box FERC Relicensing
Panel Discussion: Elements and Examples of Successful Collaborative Outcomes Alvin Thoma, PG&E Stafford Lehr, CDFW Beth Livingston, USFS Curtis Knight, CalTrout
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Session I: Stream Management and Restoration in California Collaborating for the Future
1:00pm 3:00pm Schoolhouse Moderator: Joe Merz1 and Rocko Brown2
1 2
Cramer Fish Sciences, University of Santa Cruz, Engineering Geomorphologist, UC Davis, ESA
These two sessions will showcase different areas of expertise and knowledge in both fisheries science and regulatory policies to inform the audience about roles to improve the conservation and sustainability of fishery resources and aquatic ecosystems including role as leaders, followers, team members, and advocates. Sessions will be organized based on topic that will explore the work of our active members and non-members alike in helping achieve the mission of the AFS. California contains 11% of the US population and provides its largest economy. Virtually every major California watershed is now regulated with human inhabitants expanding into each drainage. Over 32 California fish species are presently listed under federal and state endangered species regulation. If there is one take home message from centuries of California land and water use it is that collaboration is essential to effective riverine ecosystem management and restoration. How do we manage and rehabilitate valuable freshwater resources while recognizing the multi-use aspects of virtually every facet of California water? This session presents examples from regulators, managers, and fisheries and physical scientists working together in California watersheds on projects to benefit fish resources within the setting of multiple uses.
Time
1:00pm 1:20pm 1:20pm 1:40pm 1:40pm 2:00pm 2:00pm 2:20pm 2:20pm 2:40pm 2:40pm 3:00pm
Speaker
Phil Stevens
Planning for implementation
John Hannon Tom Gohring
Collaboratively improving Salmonid spawning, rearing, and passage in Central Valley Project rivers Collaboration and resource management in highly populated California
Laurel Marcus
Fish friendly farming - Collaborative restoration and management
Chester Anderson Carol Mahoney
Coordination and communication in the middle San Joaquin River watershed
Using the F-Word: FISH
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Session II: Stream Management and Restoration in California Collaborating for the Future
3:00pm 5:00pm Schoolhouse Moderator: Joseph Merz1 and Rocko Brown2
1 2
Principal Scientist in Restoration Ecology, Cramer Fish Science; Assistant Adjunct Professor, UC Santa Cruz Engineering Geomorphologist, UC Davis, ESA
Time
3:00pm 3:20pm
Speaker
BREAK
3:20pm 3:40pm
Zac Jackson
Doubling anadromous salmonid and sturgeon populations in the California Central Valley; 25 years of challenge and success
3:40pm 4:00pm
Rene Henery
Collaborative kernels: Advances in the conservation and restoration of mountain meadows and streams in California
4:00pm 4:20pm
Jose Setka
Evolution on the Mokelumne River: from litigation to collaboration
4:20pm 4:40pm
Joseph Merz
Merced River Ranch: Collaboration on a science based, community-driven restoration project
4:40pm 5:00pm
Steve Rothert
Collaborating in rough seas: can the Yuba Salmon Forum succeed in restoring Yuba salmon?
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Sessions I & II: Science Informing Green Sturgeon Restoration

1:00pm 5:00pm Central Pacific Moderator: Andrea Schreier, Assistant Project Scientist, Genomic Variation Laboratory, UC Davis
Time
1:00pm 1:20pm
Speaker
Ethan Mora
Estimating the abundance and distribution of spawning green sturgeon using a DIDSON acoustic camera
1:20pm 1:40pm
Alicia Seesholtz
Are green sturgeon only found in the Feather River during wet water years? Myth busters and its implications...
1:40pm 2:00pm
Emily Miller
Seasonal distribution of green and white sturgeon in the San Francisco Bay, Delta, and Sacramento River
2:00pm 2:20pm
Josh Strange
Status and origin of green sturgeon of Eel River Basin: Myth or mystery?
2:20pm 2:40pm
Olaf Langness
Green sturgeon research in the Washington and Oregon coastal estuaries
2:40pm 3:00pm
Andrea Schreier
Non-natal estuary preferences of SDPS and NDPS green sturgeon water diversions
3:00pm 3:20pm 3:20pm 3:40pm
BREAK Jamilynn Poletto

The efficacy of deterrents and pipe modifications in reducing entrainment of green sturgeon at unscreened water diversions
3:40pm 4:00pm
Mike Thomas
Movement behavior of juvenile green sturgeon in the Central Delta
4:00pm 4:20pm
David Woodbury
Is recovery of green sturgeon possible?
4:20pm 5:00pm
PANEL DISCUSSION
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Sessions I & II: Acoustic Telemetry

8:00am 12:00pm Central Pacific Moderator: Russell Bellmer
Time
8:00am 8:20am
Speaker
Russell Bellmer
Dual frequency identification sonar (DIDSON) is an acoustic camera presently being deployed state wide to assess salmonid populations under the California Coastal Salmonid Monitoring Plan
8:20am 8:40am 8:40am 9:00am
Mathew Metheny Zachary S. Larson
Using DIDSON in life cycle monitoring on Redwood Creek, Humboldt County Use of dual frequency identification Sonar (DIDSON) to monitor steelhead escapement in the Smith River, California
9:00am 9:20am
Benjamin J. Atencio
Estimating coho salmon and steelhead escapement for Lagunitas Creek using DIDSON technology
9:20am 9:40am
Matthew R. Johnson
Using DIDSON during turbid water periods to compliment overhead and underwater video to estimate Chinook salmon escapement in tributaries of the Upper Sacramento River
9:40am 10:00am
Dave Vogel
Use of DIDSON to evaluate fish screens, water diversions, juvenile salmon rearing, and predatory fish
10:00am 10:20am 10:20am 10:40am 10:40am 11:00am
BREAK Sam Bankston

DIDSON in Southern California streams: challenges and potential solutions
Ryan Cuthbert
Vaki Riverwatcher Case Studies: Functionality improvements to curtail limitations
11:00am 11:20am 11:20am 11:40am
Joshua Strange
Mobile applications of DIDSON sonar for green sturgeon research
Gretchen Umlauf
Alternative use of sonar in detection and discernment of fish species in short range, turbid areas, with Adaptive Resolution Imaging Sonar (ARIS) short range units
11:40am 12:00pm
PANEL DISCUSSION
22

Session I: Can we link salmonid biology with freshwater habitat for successful restoration?
8:00am 10:00am Schoolhouse Moderators: Laurie A. Earley1 and Sean P. Gallagher2
1 2
Battle Creek and Clear Creek Restoration Program, U.S. Fish and Wildlife Service Coastal Watershed Planning and Assessment Program, California Department of Fish and Wildlife
The purpose of this half-day symposium is to bring together experts on restoration ecology to discuss how understanding the linkage between salmonid freshwater habitat and biology can be used to improve restoration prescriptions. A variety of restoration efforts are planned or have been completed up and down the West Coast. The goal of these projects is focused on the recovery of salmonid populations. Project objectives include, providing fish access to higher quality or improved habitat, or creating new spawning and rearing habitat. Addressing the biological needs of salmonids may prove to be essential in the success of restoration efforts. This symposium is an opportunity to evaluate ongoing and completed restoration actions. The knowledge gained from research or monitoring on the effectiveness of these projects is critical to understanding whether restoration prescriptions have been beneficial. Understanding these projects success, challenges, and pitfalls will help to improve the future of salmonid restoration. This symposium will focus on projects that used information on salmonid biology in the restoration design and implementation. Presentations will provide insight for future projects by highlighting information on project design and monitoring directed at fish habitat responses. This symposium is intended to continue the dialogue on how to improve salmonid restoration and monitoring based on the lessons learned from projects throughout California and the Pacific Northwest.
Time
8:00am 8:20am
Speaker
Mike Wallace
Response of juvenile salmonids to habitat restoration in the stream-estuary ecotone of Humboldt Bay
8:20am 8:40am
Mark Gard
Tuolumne, Stanislaus, and Yuba River floodplain versus flow relationships
8:40am 9:00am
Gregory M. Andrew
Enhancing winter habitat for salmonids in Lagunitas Creek
9:00am 9:20am
Justin Wood
Ecosystem response to spawning bed enhancement in Deer Creek, Yuba River tributary
9:20am 9:40am
Jerrad Goodell
Use of redd caps and egg tubes to asses spawning habitat of Chinook salmon
9:40am 10:00am
Joseph Merz
Restoration under suboptimal conditions: Examples from Chinook salmon and steelhead projects in the California Central Valley
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Session II: Can we link salmonid biology with freshwater habitat for successful restoration?
10:00am 12:00pm Schoolhouse Moderators: Laurie A. Earley1 and Sean P. Gallagher2
1 2
Battle Creek and Clear Creek Restoration Program, U.S. Fish and Wildlife Service Coastal Watershed Planning and Assessment Program, California Department of Fish and Wildlife
Time
10:00am 10:20am
Speaker
BREAK
10:20am 10:40am
Laura Valoppi
Successes and challenges of fisheries resources in a large restoration project
10:40am 11:00am
Neil Lassettre
Dry Creek Habitat Enhancement Project: Linking habitat conditions to salmonid ecology and production through monitoring and adaptive management
11:00am 11:20am
Matthew Deitch
A process for hydrologic restoration for salmonids in coastal California
11:20am 11:40am
Stephen Swales
Back from the brink - Challenges, collaborations and solutions for salmon recovery in California
11:40am 12:00pm
PANEL DISCUSSION
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Sessions I & II: Native Fishes
8:00am 12:00pm Steamboat Moderator: Wayne Lifton, Senior Aquatic Ecologist, Cardno Entrix
Time
8:00am 8:20am
Speaker
Larry Brown
Implications of water temperatures from climate change projections for delta smelt in the Sacramento-San Joaquin Delta, California
8:20am 8:40am
Carl L. Demetropoulos
Abundance and conditions of the federally threatened Santa Ana sucker ( Catostomus santaanae) in Big Tujunga Creek; Influence of habitat dynamics and benthic macroinvertebrate species and composition
8:40am 9:00am 9:00am 9:20am 9:20am 9:40am
Stewart B. Reid
Exploring the historical, current and future distribution of Pacific lamprey in California
Shawn D. Chase Wayne Lifton
Maximizing habitat for native species in flood control channels Investigations into hardhead (Mylopharodon conocephalus) life history in the San Joaquin drainage
9:40am 10:00am
Dennis E. Cocherell
Physiological tools for guiding native fish management near hydroelectric power generation facilities: a case study of hardhead minnows
10:00am 10:20am 10:20am 10:40am
BREAK Christopher J. Donohoe

Migratory histories, maternal origin, and connectivity of rainbow trout ( Oncorhynchus mykiss) from the Lower Mokelumne River
10:40am 11:00am 11:00am 11:20am 11:20am 11:40am
Rick Wilder
Potential effects of future climate change on salmonids in Californias Central Valley
Nicolas Retford
Ocean conditions and growth rates of Scott Creek steelhead
Amber Manfree
A new look at the fishes of Suisun Marsh: visualizing spatiotemporal data with animated maps
11:40am 12:00pm
Megan Sabal
Interactive effects of a non-native predator and habitat alterations on native juvenile salmon
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Sessions I & II: General Symposium
12:00pm 5:00pm Schoolhouse Moderator: Michael Carbiener, Senior Fisheries Biologist, URS Corporation
Time
1:00pm 1:20pm
Speaker
Adam Cockrill
Impacts of surface water diversions for marijuana cultivation on aquatic habitat in four Northwestern California watersheds
1:20pm 1:40pm
William Beckon
How to estimate trophic position of fish from lag in contaminant bioaccumulation
1:40pm 2:00pm
Andrew Schultz
Predation and gut evacuation rates as measured by acoustic tags in the Tracy Fish Collection Facility Primary Channel How the advancement in field data collection devices can help you get more work done in less time with better results
2:00pm 2:20pm
Shaun Minton
2:20pm 2:40pm
David Delaney
Challenges of predicting the movement of juvenile steelhead in the Sacramento-San Joaquin Delta
2:40pm 3:00pm
C. Meiling Roddam
Rearing location of juvenile Chinook salmon within the Shasta River basin as determined by otolith strontium isotopic ratio analysis
3:00pm 3:20pm 3:20pm 3:40pm
BREAK Jim Reynolds

Electrofishing with spheres, rings and rods: Electrical fields of three common electrodes
3:40pm 4:00pm
Rob Titus
Is the Sacramento River fall-run Chinook salmon sport fishery self-regulating?
4:00pm 4:20pm
Catherine Karp
Summary of 2013 Juvenile Salmonid Acoustic Telemetry Behavior Study at the Bureau of Reclamation Tracy Fish Collection Facility, Tracy, CA
4:20pm 5:00pm
Question and Answer Session
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Sessions I & II: San Joaquin River Restoration Program

12:00pm 5:00pm Central Pacific Moderator: Elif Fehm-Sullivan, Fisheries Biologist, NMFS
Time
1:00pm 1:20pm
Speaker
Elif Fehm-Sullivan
Introduction of session and history of San Joaquin River Restoration Program
1:20pm 1:40pm
John Netto
Timelines and deadlines: Aligning settlement deadlines, project schedules, and Salmon reintroduction on the San Joaquin River
1:40pm 2:00pm
Rhonda Reed
Replacing something that doesn't exist: Regulatory, social, and biological issues for reintroduction of Chinook Salmon into the San Joaquin River
2:00pm 2:20pm
Blair Greimann
Quantifying existing chinook salmon rearing and migration habitat for the San Joaquin River Restoration Program San Joaquin River floodplain habitat: modeling juvenile Chinook salmon needs
2:20pm 2:40pm
Paul S. Bergman
2:40pm 3:00pm 3:00pm 3:20pm 3:20pm 3:40pm
PANEL DISCUSSION BREAK Nathaniel Butler

Availability of thermal stratification and thermal refugia in the middle San Joaquin River system
3:40pm 4:00pm
Leslie Mirise
Restoration leads to innovation: The Arroyo Canal and Sack Dam multi-species transport channel/fish ladder
4:00pm 4:20pm
Michelle Workman
Fisheries investigations conducted in the San Joaquin River Restoration area and their relation to salmon reintroduction in the San Joaquin River
4:20pm 4:40pm
Kyle Griffiths
Trends in piscivory in an altered environment of the San Joaquin River
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Sessions I & II: Fish Genetics
12:00pm 5:00pm Steamboat Moderator: Scott Blankenship, Senior Scientist, Cramer Fish Sciences
Time
1:00pm 1:20pm 1:20pm 1:40pm
Speaker
Scott Blankenship Michael Hellmair
Genetic identification of salvaged winter-run Chinook salmon at SWP and CVP facilities Low genetic diversity and reduced life history variation increase extinction risk within insular populations of an endangered fish
1:40pm 2:00pm
Molly Stephens
The power of SNPs to understand past stocking and contemporary status of native trout populations
2:00pm 2:20pm
Anna Sturrock
Life history portfolio within salmon populations: When do different outmigration phenotypes contribute?
2:20pm 2:40pm
Jesse Wiesenfeld
Riverscape genetics identifies two genetically divergent groups and a contact zone in Klamath River speckled dace (Rhinichthys osculus)
2:40pm 3:00pm
Patricia Brandes
Genetics data and efficiency testing for deriving abundance of four runs of juvenile Chinook salmon at Chipps Island
3:00pm 3:20pm 3:20pm 3:40pm 3:40pm 4:00pm
BREAK Gregg Schumer Scott Brandl

Using genetics to enhance and integrate existing Delta monitoring programs Quantifying incidence of predation using genetic barcodes and its potential as a near realtime ecological monitoring tool
4:00pm 4:20pm
Chris Hogle
Dont need a mate, just need a trout: genetic and demographic structure of three western pearlshell mussel (Margaritifera falcata) populations in the western Great Basin
4:20pm 4:40pm 4:40pm 5:00pm
Virginia Afentoulis Paul S. Bergman
Efficacy test of a tag designed to signal when a fish has been consumed A pilot mark-recapture study using spot patterns of Oncorhynchus mykiss in the Stanislaus River, California
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Oral Presentation Abstracts

Efficacy test of a tag designed to signal when a fish has been consumed
Virginia Afentoulis, Andrew Schultz
California Department of Water Resources, 5280 Bruns Road, Byron, CA 94514, (209) 833-0125, vafentou@water.ca.gov
Prototype HTI acoustic predation tags designed to indicate an acoustic tagged fish had been eaten by a predator were tested by DWR and Reclamation staff at the Tracy Fish Collection Facilitys Tracy Aquaculture Facility. Six adult striped bass (> 400 mm FL) were each sequentially fed ten Chinook salmon with implanted predation tags. Initial feeding time to predation tag activation time, was recorded for 54 of the 60 predation tags (6 tags failed to activate). Average time for a tag to activate was 57:30:59 (range: 22:18:00 to 140:01:00). Control predation tags (tags turned on but not in predation indication mode) were surgically implanted in to two groups of ten control Chinook salmon. The control Chinook salmon were held for at least 30 days post-surgery to check for effects of the predation tag on fish health and recovery from surgery. There were 3 mortalities within 2 weeks after the surgical implantation. There were no false positives in the control fish, meaning that the tags did not activate in the target species. Predation tags are a promising new technology for determining the fate of acoustically-tagged salmonids. Once field tested, these tags could be used in many applications to understand the magnitude of predator impacts on salmonids near manmade structures.
restoration of riparian, floodplain, wetland, and instream habitats that benefit threatened and endangered species including salmon, sturgeon, steelhead, Delta smelt, and numerous other native species. Much of the land in the watershed is prime agricultural land, a significant contributor to employment in the watershed, the worlds food system, and the economy. There is substantial resistance from the agricultural community to the proposed restoration projects in large part because of the manner in which they have been and are being proposed and the lack of coordination with and understanding of the agricultural community. On the other hand, resistance from the agricultural community is due, in large part, to misconceptions about how the restoration projects will impact the agricultural systems in the watershed. In reality, much of the habitat restoration being proposed would have little if any impact to the agricultural system and may even benefit the agricultural community if the proposed projects were coordinated with the agricultural communities needs for improving irrigation and drainage water quality, protecting access to water resources, and dealing with invasive and harmful pests and weeds. In this presentation I will briefly review coordination and communication strategies and opportunities that State and Federal agency staff may implement with local stakeholders so restoration of habitats may occur in a more timely, efficient and economical manner, coordinated with the needs of the agricultural community.
Coordination and communication in the Middle San Joaquin River Watershed

Chester Anderson
Watershed Coordinator, Middle San Joaquin River Watershed, East Stanislaus Resource Conservation District, chester@eaststanrcd.org
Enhancing winter habitat for salmonids in Lagunitas Creek

Gregory M. Andrew, Eric Ettlinger, and Bill Trush
Marin Municipal Water District 220 Nellen Avenue; Corte Madera, California 94925, (415) 945-1191, gandrew@marinwater.org.
The East Stanislaus Resource Conservation District is drafting a Coordination Strategy for the Middle San Joaquin River Watershed that includes the lower Merced, Tuolumne and Stanislaus Rivers. The purpose of the Strategy is to facilitate the restoration of habitats coordinated with the needs of the agricultural community. Proposals for the restoration of habitat in the watershed come from outside the watershed, primarily from State and Federal agencies, and include
Lagunitas Creek is a coastal drainage that supports the largest population of coho salmon (Oncorhynchus kisutch) in Central California and a robust population of steelhead (O. mykiss). Winter habitat has been identified as the limiting factor for coho and steelhead populations in the watershed. With funding provided by the California Department of Fish and Wildlife, Fisheries Restoration Grant Program, an assessment of winter habitat and site specific designs to enhance
29

winter habitat in Lagunitas Creek have been completed. Specifically, this planning and design effort has been aimed at developing ways to increase the creeks winter carrying capacity for salmonids through increased parr to smolt survival. The assessment hypothesized two main causes of winter habitat problems in Lagunitas Creek: a deep, confined channel with elevated velocities during storms and even at winter base flows; and reduced inundation of floodplain and side channel habitat for salmonids. Approaches to designing winter habitat enhancement projects have included: reconnecting and reestablishing historic side channels within the floodplain; increasing overbank and off channel flooding; and providing abundant cover within the base flow channel and the reestablished floodplain habitats. Constraints and design considerations have included: preventing fish stranding, avoiding creating habitats for invasive predators, and ensuring good water quality conditions are maintained. Fortunately, much of Lagunitas Creek flows through State and Federal park lands that provide realistic opportunities to manipulate the riparian corridor to enhance habitat. There has also been a great deal of collaboration among a multitude of agencies, organizations, and individuals interested in seeing successful salmonid restoration in Lagunitas Creek. This project is a good example of winter habitat enhancement that is a priority for salmon recovery in the coastal rivers and streams of California. stations to determine adult coho and steelhead escapement. Dual-frequency identification sonar (DIDSON) technology was identified by CDFW as a potential non-intrusive survey method for meeting the adult counting station requirement. In addition, escapement estimates using a DIDSON camera could be compared to current adult escapement estimates provided by MMWD. During the winter of 2012-2013, a DIDSON camera was installed in Lagunitas Creek by Point Reyes National Seashore Association (PRNSA) staff. Initial assembly, instillation, and site selection proved inadequate to produce accurate escapement results. By January of 2013 PRNSA staff solved most of the factors that had prevented the DIDSON from being used as an adult counting station. Although a 20122013 coho escapement estimate could not be calculated using the available DIDSON footage, a steelhead escapement estimate was calculated for the first time on Lagunitas Creek. The DIDSON was operational 81% of the time from December 13, 2012, to April 29, 2013. DIDSON footage review recorded 12,153 fish passage events, with 5,476 upstream passage events, 5,349 downstream events, and 1,328 fish milling events. Peak upstream and down stream migration both occurred on the same day, March 28, with 192 upstream and 212 downstream events. Seventy percent of all fish passage events occurred at night. It is anticipated that operation of the DIDSON camera at its current location on Lagunitas Creek will produce the imagery needed to calculate adult escapement estimates for both coho and steelhead during the 2013-2014 spawning period.
Estimating coho salmon and steelhead escapement for Lagunitas Creek using DIDSON technology
Benjamin J. Atencio, Michael Reichmuth
Point Reyes National Seashore Association and National Park Service Inventory and Monitoring Program, San Francisco Bay Area Network, (415) 464-5206, benjamin_atencio@partner.nps.gov
Reservoir management strategies to reduce fish mercury levels: An integral part of the statewide reservoir mercury TMDL
Carrie Austin
San Francisco Bay Regional Water Quality Control Board, 1515 Clay Street, Suite 1400 Oakland, CA 94612, (510) 622-1015, Carrie.Austin@waterboards.ca.gov
Since 1995, the Marin Municipal Water District (MMWD) has conducted long-term monitoring of adult coho salmon (Oncorhynchus kisutch) and steelhead (O. mykiss) using direct observation techniques on Lagunitas Creek. In 2012, Lagunitas Creek was selected as a life cycle monitoring station (LCMS) by the California Department of Fish and Wildlife (CDFW). A major component of LCMS is the use of adult counting
Mercury is negatively impacting many waters in California. Currently, about 75 lakes and reservoirs in California are officially designated as impaired by mercury because they have fish mercury concentrations that pose risks to human and wildlife consumers. Data suggest that fish mercury levels are elevated in about half of all California lakes and
30

reservoirs sampled. Mercury impairment is due to several interrelated factors: inorganic mercury sources; conditions in reservoirs that cause the conversion of inorganic mercury to methylmercury and its subsequent bioaccumulation in the food web; and fish species present. Reservoir creation and management may exacerbate the mercury impairment by increasing methylmercury production and bioaccumulation. This is one of two presentations on the State Water Boards development of a Statewide Mercury Control Program for Reservoirs. Most mercury total maximum daily loads (TMDLs) across the nation rely on source controls as their primary actions to reduce fish mercury concentrations. However, an analysis of the controlling factors of fish mercury concentrations in California reservoirs indicates that source control alone will not fix the problem in a reasonable amount of time for many of the reservoirs. Actions to reduce mercury methylation and food web bioaccumulation are likely necessary to reduce mercury levels in reservoir fish to safe levels. Water Board staff would like to encourage innovation and inter-agency cooperation to develop reservoir water chemistry and fisheries management techniques to reduce fish mercury, in conjunction with mercury source controls. In this presentation, Water Board staff will present this novel approach to a control program. There are several inherent limitations of using DIDSON in Southern California. These include: shallow and flashy rivers, high turbidity, sizing error, and species identification. Shallow water causes sound waves to reflect off of the surface and bottom adding acoustic noise to images, making fish difficult to distinguish. The flashy nature of rivers can create high turbidity, making fish identification more challenging. While one of DIDSONs major benefits is its ability to see through turbid water, image quality degrades quickly as turbidity increases. There is also error in fish sizing due to cross range pixel size which increases with distance from the sonar unit. Sizing error is less noticeable when sizing large fish; however we are interested in identifying smolts and distinguishing them from other small fish. In this instance the sizing error can be significant. Possibly the largest difficulty in monitoring steelhead passage in Southern California is species identification. In streams with species of overlapping size it is difficult to determine whether a fish seen on the DIDSON is your target species or another. We are working on solutions to several of these problems. First, we tested the use of concentrator lenses to improve shallow water DIDSON images but this didnt provide significant improvements to image quality. We are also developing a method for species identification and are experimenting with projection boards. We will use a projection board in the Ventura River during the 2013-2014 season to determine whether this is a viable option for species identification in Southern California streams.
DIDSON in Southern California streams: challenges and potential solutions

Sam Bankston, Heidi Block, Patrick Riparetti, Mary Larson, Chris Lima, Dana McCanne
Pacific States Marine Fisheries Commission, 1933 Cliff Drive #9, Santa Barbara CA 93109, California Department of Fish and Wildlife, 4665 Lampson Ave. C, Los Alamitos CA 90720, (805) 962-8230, SBankston@psmfc.org
How to estimate trophic position of fish from lag in contaminant bioaccumulation.

William N. Beckon
U. S. Fish and Wildlife Service, 2800 Cottage Way, Suite W2605, Sacramento, CA 95825-1846. (916) 414-6597, William_Beckon@fws.gov.
The California Department of Fish and Wildlife in cooperation with Pacific States Marine Fisheries Commission has begun a program to monitor endangered Southern California steelhead using dual frequency identification sonar (DIDSON). DIDSON can be useful in monitoring fish passage; however it is important to be aware of its limitations.
For bioaccumulative contaminants, such as selenium, efforts to predict concentrations in organisms at upper trophic levels, based on measurements of environmental exposure, are confounded by the appreciable amount of time it may take for bioaccumulation to occur through various pathways and across several trophic transfers. Yet studies of bioaccumulation have hitherto generally overlooked
31

this lag time, using temporally matched samples of water and tissue, effectively making the unrealistic assumption that bioaccumulation is instantaneous. The study summarized here offers a remedy for this deficiency, demonstrating a simple, objective method of automatically estimating the time required for bioaccumulation, and taking this lag into account to improve predictive modeling of bioaccumulation. This method uses a history of measurements of environmental exposure and tissue concentrations of a contaminant to systematically test a large array of potential lag characteristics (both central tendency and spread of lag), selecting the lag that provides the best regression. The method is demonstrated here using an unusually long-term data set of selenium measurements in water and aquatic organisms in sloughs in the San Joaquin Valley in California. Results indicate that, as expected, more time is required for selenium to bioaccumulate in organisms at higher trophic levels than in those at lower trophic levels. For example, the lag time for the piscivorous largemouth bass (Micropterus salmoides) may be more than one year, but only about one month for the filter-feeding threadfin shad (Dorosoma petenense). Also as expected, omnivorous organisms display a broader spread in lag time than more specialized feeders. Therefore, the method presented here not only provides a tool for improved prediction of contaminant effects and for more precise targeting of contaminant regulation, it also offers a novel means to estimate both the average trophic level of an organism and its trophic spread (degree of omnivory), when these characteristics are otherwise poorly known. increasingly demands more water and other natural resources, the ability of natural resource managers to conserve these resources will be based, in part, on their ability to maintain and restore watershed ecological processes based on scientific monitoring. Californias salmon and steelhead populations have experienced drastic declines leading to both ESA and CESA listing of many coastal stocks (Good et al. 2005, Williams et al. 2011, CDFG 2002). California has experienced pressure from the federal government, other Pacific States, fisheries organizations, and communities to improve status and trend monitoring of coastal salmon and steelhead. Of the four National Marine Fisheries Services Viable Salmonid Population (VSP; McElhany et al. 2000) parameters (abundance, spatial distribution, productivity, and diversity), adult abundance is the most fundamental. Establishment of DIDSON counting stations under the California Coastal Salmonid Monitoring Plan (Adams, et.al. 2011) in key locations will enable CDFW to obtain vital adult return data to inform State, Trans-State, and federal management and recovery decisions. Since 2009, DIDSONs have been installed in numerous California streams to enumerate adult salmon and steelhead during upstream migration. This presentation reports on the results of initial deployments of DIDSON units across California for the purpose of counting returning anadromous salmonids. We will describe the projects using DIDSONs, their location, the stated purpose of each project, and progress made to date toward project goals. This is the first comprehensive report of the use of DIDSON devices employed as part of the California Coastal Salmonid Monitoring Plan and for other uses.
Dual frequency identification sonar (DIDSON) is an acoustic camera presently being deployed state wide to assess salmonid populations under the California Coastal Salmonid Monitoring Plan
Russ Bellmer, Krissy Atkinson, and Micheal Lacy
California Department of Fish and Wildlife, Fisheries Branch, 830 S Street, Sacramento, CA 95814, (916) 327-8850, Russ.Bellmer@wildlife.ca.gov
A pilot mark-recapture study using spot patterns of Oncorhynchus mykiss in the Stanislaus River, California
Paul S. Bergman, Joseph E. Merz, David G. Delaney, Clark Watry
Cramer Fish Sciences, 13300 New Airport Rd. Suite 102, Auburn, CA 95602, pbergman@fishsciences.net
Anthropogenic alteration of landscapes have negativity altered hydrologic processes in a manner that have altered the formation of stream habitat and affected the viability of Salmonid species dependent on naturally functioning streams systems. As societies
Recent listings of numerous salmonid populations under various regional, national, and international protections, including U.S. Endangered Species Act, has increased the need to reduce direct handling or otherwise minimize impacts from invasive techniques for monitoring populations. External, natural markings such as stripes, spots, and damage to extremities
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associated with random nonrelated incidences (predator attacks, boat collisions, etc.) have been used by scientists to track individual animals, including fish species, for many years. Many salmonids have black spots that can be quite distinctive in the head region and remain throughout the life of an individual making them a potentially valuable natural marking tool for fisheries research applications. We conducted a pilot study to determine the efficacy of using head region spot patterns for a mark-recapture analysis to ultimately estimate the population size of Oncorhynchus mykiss residing immediately below Goodwin Dam on the Stanislaus River. We used spotrecognition software to analyze photographic images of fish spot patterns to identify O. mykiss individuals that were captured by hook-and-line sampling throughout March through August 2010. We used a population analysis (POPAN) formulation of the Jolly-Seber model to estimate the daily population sizes of O. mykiss. A blinded repetition of the spot pattern analysis by two different analysts resulted in identical detection histories of imaged fish, with only 5 of the 134 fish being recaptured (recapture rate of only 3.7%). Population estimates ranged from 126 (SE = 57) up to 426 (SE=205), and peaked at the end of June and beginning of July 2010. This study shows strong evidence that salmonid spot patterns can be used effectively to conduct mark-recapture studies, and could potentially be useful to not only estimate population abundance, but also examine survival, population growth, and rates of anadromy. timing and size, survival, growth, migration speed, and habitat requirements, and (2) use the ESHE model to estimate the suitable rearing and emigration habitat required to support future populations of San Joaquin River spring-run and fall-run Chinook salmon as they rear and emigrate downstream through the SJRRP restoration reaches. In this presentation, we will describe some of the general assumptions of the model including, survival, growth and migration speed and results from the models application for the SJRRP.
Genetic identification of salvaged winter run Chinook salmon at SWP and CVP facilities
Scott Blankenship1,2, Gregg Schumer1,2, Bradley Cavallo1, Kevin Reece3
1
Cramer Fish Sciences, Genidaqs, West Sacramento, CA, 2 scott.blankenship@fishsciences.net; College of Agriculture and Environmental Sciences, University of California, Davis; 3 Califonia Department of Water Resources, West Sacramento, CA 95691.
San Joaquin River floodplain habitat: modeling juvenile Chinook salmon needs
Paul S. Bergman, Joseph E. Merz
Cramer Fish Sciences, 13300 New Airport Rd. Suite 102, Auburn, CA 95602, pbergman@fishsciences.net
We applied the Emigrating Salmonid Habitat Estimation (ESHE) model to the San Joaquin River Restoration Program (SJRRP) restoration reaches to define the minimum land area required to support rearing and emigration habitat for juvenile Chinook salmon (Oncorhynchus tshawytscha). To accomplish this, we employed production from minimum viable population targets set for spring- and fall-run Chinook salmon as defined in the SJRRP Fisheries Management Plan. The tasks of this study were to (1) use the best available data (San Joaquin Basin when available) to parameterize ESHE model relationships for initial
Water exports from the South Delta cause incidental take of juvenile salmonids, potentially contributing to jeopardy of ESA-listed species. While the export loss functions essentially estimate the total fish mortality given the number of fish observed at salvaged facilities, a foundational component of these calculations is the determination of which salvaged individuals are older, as defined by length-at-date criteria (i.e., the Delta Model). NOAAs RPA define an older juvenile as an individual that resides above the lower boundary of winter run length-at-date criteria. Yet, the Delta Model is known to be ambiguous regarding race determination. The failure of the length-at-date model to accurately categorize race creates considerably uncertainty (variance) in the estimation of loss density. We were charged with using genetic methods to determine the population of origin for juveniles categorized as older by the Delta Model, as well as individuals that fell outside the winter run length-atdate criteria. The objectives of this genetic project are intended to directly target (and reduce) one source of uncertainty in the estimation of loss at salvage facilities. We analyzed juveniles captured 2010-2013 using current SNP locus panel and reference baselines from SWP and CVP water diversion facilities. As expected a substantial fraction of Model pronounced winter run were not winter run given genetic identity. Additionally, we report statistically significant differences in winter run occurrence across years (for
33

same facility) and within year (between facilities). The current regulatory process governing ESA-listed fish impacts at diversions facilities should be altered to reflect technical advances in population identification.
Quantifying incidence of predation using genetic barcodes and its potential as a near real-time ecological monitoring tool
Scott Brandl, Gregg Schumer, Brian Schreier, J. Louise Conrad, Bernie May, Melinda Baerwald
Genomic Variation Lab, UC Davis. 1 Shields Ave, Davis, CA 95616, scbrandl@ucdavis.edu.
Genetics data and efficiency testing for deriving abundance of four runs of juvenile Chinook salmon at Chipps Island
Patricia Brandes, Brian Pyper, Tommy Garrison, Steve Cramer, Michael Banks, Dave Jacobson
USFWS, 850 S. Guild Ave, Suite 105, Lodi, CA 95240, (209) 334-2968 x308, Pat_Brandes@fws.gov
Four runs of juvenile Chinook salmon migrate from the upper river through the Sacramento River and Delta to reach the ocean. The four runs of Chinook salmon are winter, spring, fall and late-fall. Juveniles from the four runs of salmon are indistinguishable in the field, but managers use a length-at-date criterion to distinguish juvenile winter and spring run salmon since they are federally listed as endangered or threatened and are the target of management actions. The length- at- date criteria uses the fork length of individual juvenile salmon on a given catch date to assign run. The lengthat-date criteria results in many false positives for both winter and spring run resulting in an overestimate of abundance at Chipps Island. This project collected tissue samples from juvenile Chinook salmon caught at Chipps Island and determined run using a set of 21 microsatellites called HSMC21. Sampling at Chipps Island was conducted two to three days per week by the U.S. Fish and Wildlife Service as part of the Interagency Ecological Program for the San Francisco Estuary. A key component of the project was to estimate efficiency at Chipps Island for the expansion of catch by run to abundance. Since it was not clear which method for estimating efficiency was superior, four methods of estimating efficiency were evaluated for expanding catch to abundance for each run. Results indicated very low abundance of late-fall, winter and spring run relative to fall run. Abundance for all four runs was lowest in 2008, while the highest abundances were in 2010 or 2011, for the four years estimated. Accuracy and precision depended critically on which value of trawl efficiency was used with roughly a 2 fold difference among the three empirical estimates.
Predation on larval fish may be an important factor in the decline of delta smelt and other species in the San Francisco Estuary-Watershed. Visual gut content analysis only shows us part of the picture, with a bias toward identification of bony or undigested specimens. Genetic gut content analysis avoids these biases by identifying prey species genetic barcodes from predator gut contents. The sensitivity of the method allows us to identify prey composed of soft tissue and prey long after they have been ingested. We are currently investigating the frequency of predation by non-native bass and the native Sacramento pikeminnow on larval and sub-adult threatened and endangered species using quantitative PCR. The data on incidence of predation will be used to identify locations and environmental parameters associated with unwanted predation on atrisk species. With this data, habitat restoration efforts can be fine-tuned to minimize danger to at-risk species. New technology is making near real-time ecological monitoring an attainable goal. Our current project incorporates genetic detection of ten prey species in four predator species using a new high-throughput platform. Increased sample sizes, simultaneous detection of a dozen or more species and fast turnover time makes using qPCR as an ecological monitoring tool feasible.
Implications of water temperatures from climate change projections for Delta Smelt in the Sacramento-San Joaquin Delta
Larry R. Brown, R. Wayne Wagner, Lisa Komoroske, Tara Morgan-King, Nann A. Fangue, Jason T. May
Larry R. Brown, U.S. Geological Survey, Placer Hall, 6000 J St., Sacramento, CA 95819-6129, (916) 278-3098, lrbrown@usgs.gov
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We assessed the possible effects on Delta Smelt (Hypomesus transpacificus) of water temperatures calculated from four 100-year scenarios of climate change at nine locations in the Sacramento-San Joaquin Delta. Results from two regional climate models at two levels of greenhouse gas emissions were used to calculate water temperatures, using location-specific regression models. We compared modeled daily maximum water temperatures to recently derived laboratory measurements of thermal maxima for four life stages of Delta Smelt: larvae (March-June), juveniles (June-December), adults (December-March), and spawning adults (March-May). We also compared modeled average daily water temperatures to a selected threshold of 25C, a temperature beyond which few Delta Smelt are captured in surveys. The juvenile life stage was the most vulnerable to climate change because of high summer water temperatures particularly in July and August. The upper San Joaquin River upstream of Stockton was the most unfavorable area for juveniles owing to temperatures exceeding the chronic lethal thermal maximum (CLTmax) for 50 percent mortality (27C) under even the mildest climate change scenario. The Sacramento River corridor was more favorable but water temperatures still exceeded the threshold at times. The CLTmax for 95 percent mortality (28C) and the critical thermal maximum (CTM; acute mortality) (29C) were rarely exceeded except in the upper San Joaquin River. For the most severe scenario, beyond 2060, the CLTmax for 95 percent mortality or critical thermal maximum of juveniles was regularly exceeded for several days per year at all sites, except in Suisun Bay. Exceedances of the 25C threshold were more common than exceedances of lethal temperatures, suggesting the 25C threshold may be an indicator of behavioral avoidance of areas likely to become lethal. Our results suggest that climate change is likely to reduce available habitat for Delta Smelt. system where modeling indicates stream temperature exceeds Chinook thermal tolerances between April and October. During periods of high stream temperature, thermal stratification in pools can create thermal refugia that provide cold water habitat below Chinook thermal tolerances. To determine the availability of thermal stratification and thermal refugia, this study measured river pool water temperature in the Eastside Bypass, Reach 4B2, and Reach 5 of the San Joaquin River system during summer and fall 2012. Vertical water temperature profiles were measured in 53 river pools to assess the general abundance of thermal stratification and thermal refugia. Six pool sites were also instrumented for two to three weeks with temperature sensor arrays and piezometers to evaluate diurnal and weekly trends in thermal refugia. Air temperature was a dominant control on the availability of thermal refugia in the Eastside Bypass, Reach 4B2, and Reach 5 of the San Joaquin River system. During October 2012, daily thermal stratification preserved cold water habitat along pool bottoms at all the sites instrumented. Both thermal stratification and volume of thermal refugia correlated with the daily maximum change in air temperature. These correlations occurred because when air temperature fell below pool water temperature each night, surface water cooling produced convective mixing that collapsed daily thermal stratification. Nightly cooling at the air-water surface reset the daily thermal stratification gradient and created thermal refugia along the pool bottom. In addition to air temperature, surface stream flow influenced the availability of thermal refugia. The interaction of stream flow with pool geometry determined mixing conditions in pools. In a pool with minimal complexity, increasing stream flow from 0.3 m3/s to 1.6 m3/s eliminated thermal refugia.
Availability of thermal stratification and thermal refugia in the middle San Joaquin River system
Nathaniel Butler
PO Box 9497, Berkeley, CA 94709, (408) 891-8501
Data overload: interfacing with new graphical tools for handling a data-rich environment
Jarvis Caldwell
HDR Engineering, Inc 2379 Gateway Oaks, Suite 200, Sacramento, CA 95833, (916) 679-8875, jarvis.caldwell@hdrinc.com
Water temperature is a critical water quality concern for the reintroduction of Chinook salmon (Oncorhynchus tshawystcha) in the San Joaquin River
The Federal Energy Regulatory Commissions (FERC) Integrated Licensing Process (ILP) mandates that environmental studies conducted in support of a new or renewed hydroelectric project license focus on the
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ability of potential project configurations and operations to provide balance between economic and environmental resource benefits and adverse resource effects. Current and future project configurations and operations have the potential of having broad effects on downstream flows and water temperatures, thus affecting multiple downstream resources. Instream flow and project operation models, which integrate both reservoir and riverine temperature models over long periods of record using both empirical and synthetic data, are often the cornerstone in evaluating potential effects on aquatic resources. The results of these models inform the development of potential protection, mitigation and enhancement measures included in a new or renewed license. Large-scale modeling efforts typically result in the production of thousands of tables and charts, often filed in attachments to reports or technical memoranda. The challenge to FERC licensing stakeholders is the distillation and integration of these discrete data sets to identify potential short- and longterm effects on aquatic resources. Further, additional sensitivity analyses aimed at evaluating alternative project operation scenarios on target resources can compound the quantity of data to unwieldy levels. Project-specific data visualization programs can compile data from multiple resource models, including operations, water temperature, one and twodimensional hydraulic, and habitat models. Recent advances in their development provide intuitive yet comprehensive graphical interfacing tools for licensing participants. These flexible software tools offer solutions to the common issue of data overload, and (more importantly) encourage the collaborative dialogue often stunted by the sheer volume of data and its discrete and disassociated nature. In addition, the integrated layering of model results into graphical data visualization tools gives stakeholders the opportunity to discover important ecosystem linkages which otherwise may be overlooked. The Yuba River Development Project (YRDP; Federal Energy Regulatory Commission (FERC) Project # P-2246) is engaged in FERCs Integrated Licensing Process (ILP) for hydropower licensing, with the new license expected to be issued in 2016. The lower Yuba River is unique in that an extensive fish and habitat monitoring program has been in place since 2007 as part of the Lower Yuba River Accord (Yuba Accord). As part of the Fisheries Agreement of the Yuba Accord, a river management team (RMT) was established and an extensive data collection effort was underway before ILP activities began in 2010. This has been beneficial because the RMT comprises an existing core group of applicant, agency, and non-governmental organization personnel that have been engaged in and are knowledgeable about Yuba River issues; several of the same people also are involved in YRDP ILP activities. Many of the study plans developed as part of the FERC ILP have been improved by utilizing RMT data; however, integrating the Yuba Accord and ILP activities has presented challenges due to differing participant goals and agency authorities under the two processes. As is true of many Central Valley rivers, more comprehensive data are available for adult Chinook salmon than for juvenile salmonids or steelhead. Fully assessing the effects of Yuba Accord flows and proposed YRDP FERC license on fish and fish habitat remains difficult, making it a challenge to develop adequate license conditions and measures to protect, mitigate, or enhance environmental resources.
Perspectives on design of step-pool stream channel segments

Michael Burke and Shawn Chartrand
Balance Hydrologics. 800 Bancroft Way, Suite 101. Berkeley, CA 94710, (604) 808-0146, schartrand@balancehydro.com
Yuba River Development Project FERCintegrated licensing process: U.S. Fish and Wildlife Service perspective
Elizabeth A. Campbell, Alison G. Willy
U.S. Fish and Wildlife Service, Anadromous Fish Restoration Program, 850 S. Guild Avenue, Suite 105, Lodi, CA 952403188, (916) 414-6534, elizabeth_campbell@fws.gov
Few settings within the drainage network display the interplay of fundamental geomorphic and fluvial processes more plainly than in a pristine step-pool mountain stream. This includes the coupling of hillslope and channel processes, the dissipation of energy as water flows from the mountains to the sea, and the adjustment of bedforms to inputs of water and sediment. Yet, it is only within the last 25 years through the efforts of a handful of researchers that the geomorphology of mountain stream channels in general, and step-pool streams in particular, have
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received focused attention. This research has advanced our understanding of how mountain streams are formed and maintained, and sheds light on their resilience and function. Over the same period, practitioners and land managers have constructed stream channels that were designed to emulate mountain streams, in some instances within landscape settings where such streams would not develop naturally. These applied efforts were envisioned to address an array of objectives. Among the most common are rehabilitation of discontinuities in stream gradient due to infrastructure and land use practices, and enhancement of passage conditions for aquatic species. With these objectives in particular, it is common to use the step-pool form to achieve the desired post-project conditions. The presently ongoing San Clemente Dam Removal project on the Carmel River (CRRDR), Monterey County appears to offer one of the largest experiments of step-pool morphology construction in an attempt to restore gradient and passage continuity to parts of the upper watershed. During this presentation we will briefly review the CRRDR project and dive into some of the particular details regarding development of the indicative step-pool design. decreases. The Water Agency is encouraging the development of a multistory riparian community, and the development of low flow channels that are narrower, deeper, and have a higher degree of sinuosity. These changes in management approach have been shown to incrementally improve aquatic and terrestrial habitats in maintained flood control channels. Preliminary fisheries investigations and fish relocation efforts have documented 12 native and 8 non-native species inhabiting flood control channels draining the Santa Rosa Plain. Despite the highly altered conditions of these creeks, native species comprise approximately 96 percent of the fish in these channels. Although limited by the physical, regulatory, social and infrastructural constraints on these steams, opportunities do exist to improve aquatic habitat, on both permanent and temporal timescales. So the question is this can functioning flood control channels provide habitat for native species? We believe that the answer to this question is yes.
Physiological tools for guiding native fish management near hydroelectric power generation facilities: a case study of hardhead minnows
Dennis E. Cocherell, J. J. Cech, Jr, L. C. Thompson, and N. A. Fangue
Wildlife, Fish, and Conservation Biology Department, 1088 Academic Surge, University of California, Davis, One Shields Avenue, Davis, CA 95616, (925) 963-1621, decocherell@ucdavis.edu
Maximizing habitat for native species in flood control channels

Shawn D. Chase and Keenan Foster
Sonoma County Water Agency, 404 Aviation Blvd, Santa Rosa California 95403, Shawn.Chase@scwa.ca.gov
The Sonoma County Water Agency (Water Agency) provides channel maintenance services on streams flowing across the Santa Rosa Plain. The Water Agency seeks to improve its stewardship of terrestrial and aquatic habitat along these managed streams. Most of these creeks are bordered by residential and business developments and have been straightened, widened and deepened to provide capacity necessary to reduce the risk of flooding. Because of these modifications, on-going intensive management is periodically needed to control vegetation density and sediment accumulations. Each depositional section of flood control channel is subject to varying rates of sedimentation which accumulates in predictable patterns over a predictable timeframe. Aquatic habitat available in these channels improves as sedimentation progresses while designed hydraulic capacity
The effects of river fragmentation, alteration, and flow management on native fishes have been widely studied, yet criteria are often lacking to assist managers in adapting hydropower operations to conserve native fishes. Results from laboratory-based physiological experiments can provide specific guidance on how to best manage heavily modified river systems within optimum conditions for aquatic species. Our model fish, hardhead minnow Mylopharodon conocephalus, has declined in population possibly due to dam construction with consequent temperature and watervelocity changes, and the introduction of non-native species. To address these concerns, we conducted behavioral and physiological studies of temperature preference, resting and active metabolic rates, and critical thermal maxima and minima, for both adult and
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juvenile fish acclimated to one of four environmentally relevant temperatures (11, 16, 21, or 25C). Hardhead performed well at moderate (ca. 16-21C) temperatures. Regardless of thermal acclimation history, hardhead preferred a mean water temperature of 19.4C and clearly avoided temperatures above ca. 26C. Resting metabolic rates increased with increasing acclimation temperatures in both juveniles and adults, with low to moderate thermal sensitivity. Adult active metabolic rates ranged from 209-1342 mg O2/kg/h in Brett-style respirometers at velocities from 30-90 cm/s, providing an estimate of the species maximal continuous rate of oxygen consumption (i.e., aerobic capacity). Juveniles performed poorly at cooler temperatures, refusing to swim above 10 cm/s. Hardhead lost equilibrium when rapidly exposed to water above 29.7C or below 7.4C, not including acclimation acquired zones. These results suggest that hardhead are well-suited for sustained aerobic activity over a range of flow velocities, at moderate temperatures (ca. 16-25C). However, juveniles, emerging in Spring, may not be able to perform in cold water and/or high flow velocities, providing a caution to dam managers and regulators to avoid spring and summer operations whereby juveniles experience conditions beyond those occurring in unregulated rivers. imagery interpretation. We estimated the water demand of marijuana irrigation and the potential effect water diversions could have on streamflow patterns at different scales within the watersheds. According to our estimates, water demands from marijuana cultivation have the potential to divert substantial proportions of the flow in our study watersheds, with our least impacted watershed seeing a maximum potential flow reduction of almost 60 percent, and other streams predicted to dry up entirely under certain diversion scenarios. These predictions are supported by field observations in our study watersheds documenting diminished or nonexistent flows during the summers in recent years. Diminished stream flow due to marijuana cultivation is highly likely to have lethal or sub-lethal effects on state and federally-listed fishes and further decline of sensitive amphibian species. This is the first study to quantify aquatic impacts of marijuana cultivation on a watershed scale. Conservation strategies are proposed.
Effects of boat noise on a wild, vocal Fish, Plainfin Midshipman, Porichthys notatus
Sarika Cullis-Suzuki
University of York (UK), Heslington, York YO10 5DD, United Kingdom, +1 (778) 868-1945, sarikacullissuzuki@gmail.com
Impacts of surface water diversions for marijuana cultivation on aquatic habitat in four northwestern California watersheds
Scott Bauer, Adam Cockrill, Jennifer Olson, Michael van Hattem, Linda Miller, Gordon Leppig, Margaret Tauzer
California Department of Fish and Game, 619 2nd Street, Eureka, CA 95501, (707) 441-2011, scott.bauer@wildlife.ca.gov
Large-scale marijuana cultivation has proliferated in northwestern California since the mid-1990s. The environmental impacts of marijuana cultivation appear substantial, yet have been difficult to quantify because cultivation is clandestine. We interpreted highresolution aerial imagery to estimate the number of marijuana cultivation sites, greenhouses, and plants in four watersheds in northwestern California, USA. Lowelevation fixed-wing aircraft flights and cultivation site visits in the region validated assumptions used in aerial
In response to increasing anthropogenic ocean noise, the impact of noise on marine life has become a recent topic of concern. Various studies have centered on fish, and in particular, on acoustic communication; lacking however are inquiries into impacts of noise on predatorprey interactions. Here, we focus on a highly soniferous species of Toadfish, the plainfin midshipman (Porichthys notatus) off Quadra Island, British Columbia. Through examining a wild intertidal population of P. notatus, we identify and describe the 'grunge', a previously undocumented defensive response employed by nesting male P. notatus against heterospecific predators and consisting of a lunge simultaneously coupled with a loud grunt. We further quantify predator-prey interactions under no noise, ambient and boat noise conditions. As a growing body of research suggests harmful effects of noise on individual species, our results reveal direct implications on ecosystem processes and heterospecific relationships, and are described in light of a changing marine soundscape.
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Vaki Riverwatcher case studies: functionality improvements to curtail limitations
Ryan Cuthbert
FISHBIO, 1617 S. Yosemite, Oakdale, CA 95361, (209) 8476300, ryancuthbert@fishbio.com
The Vaki Riverwatcher infrared fish counting system (RW) has been used throughout the world to monitor fish in a variety of conditions and in various unique installations. The first RWs were installed in West Coast rivers in the early 2000s. Although most of the original RW installations are still active today, many of the following adjustments have been made to improve RW functionality and operational capacity. Remote connectivity was added to decrease data collection effort at remote installations by increasing the time period between checks. An underwater camera was also added to improve identification certainty in rivers with multiple species. Portable weirs have been used to expand the operational capacity of the RW to wider, deeper rivers with fluctuating flows. A camera tunnel was configured to improve the quality of the videos/photos. Different configurations and dimensions of the infrared scanner were also implemented to accommodate more unique installations. An air-filled chamber camera housing was configured to the RW to improve the quality of video/photos during high turbidity events. Changes were also made to the RW software to allow users to record videos/photos for downstream passages without the purchase of additional equipment. Finally, cloud-based software (Riverwatcher Daily) was developed to help users share data more easily, as well as provide a platform for individuals interested in public relations. These changes have given researchers more opportunity to monitor larger rivers with multiple species under unique environmental conditions, and in unique installation configurations.
Predicting the movement of a species is important for conservation and management but remains a challenge. As part of the California Department of Water Resources Stipulation Study, we examined how well a physical model can predict the movement of acoustically-tagged steelhead (Oncorhynchus mykiss) and investigated underlying biological mechanisms limiting model accuracy. During the spring of 2012, we conducted a mark-recapture experiment to examine the movement patterns of steelhead emigrating through the south Sacramento-San Joaquin Delta. We released approximately 500 juvenile steelhead near Buckley Cove in the lower San Joaquin River. The quantitative statistical analyses determined that a purely physical model in the form of the Delta Simulation Model II Hydro Particle Tracking Model was not able to predict the movement of steelhead tags. The model greatly underestimated the steelhead tag movement rate through the study area as steelhead tags were traveling significantly greater distances than passive particles. We also documented some behaviors of steelhead that could explain the discrepancies between the passive particles and steelhead tag data. Our findings suggest that migrating steelhead exhibit a complex set of behaviors that are not captured by simple physical models. Additional studies are needed to better understand these behaviors and ultimately improve forecasting of salmonid migrations.
A process for hydrologic restoration for salmonids in coastal California

Matthew Deitch
Center for Ecosystem Management and Restoration 4179 Piedmont Avenue, Suite 325 Oakland, CA 94611, (510) 420-4565 x106, deitch@cemar.org
Challenges of predicting the movement of juvenile steelhead in the Sacramento-San Joaquin Delta
David Delaney, Paul Bergman, Bradley Cavallo, Jenny Melgo, and Kevin Clark
Cramer Fish Sciences, 13300 New Airport Rd. Suite 102, Auburn, CA, 95602, (530) 888-7773, david.delaney@fishsciences.net
In coastal California, most of the critical habitat for protected salmonids is located in small streams that are tributary to large rivers such as the Russian River. Over the past decade, attention has been given to restoring appropriate hydrologic conditions for salmonids, given impairment that human demands for water cause to streamflow. Understanding the potential for streamflow restoration requires understanding the natural geohydrological limitations and impacts that water demands place on streamflow (especially relative to the salmonid life cycle), as well as the potential for alternative methods to meet water needs and maintain
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appropriate hydrologic conditions for salmonids. We have been applying a data-driven process to restore streamflow in small critical-habitat streams tributary to the Russian River (and elsewhere). Our results indicate that streamflow impairment can be substantial and is often unexpected; and solutions are often feasible to maintain human water needs and adequate flow for salmonids. Our work also indicates the widespread need for streamflow restoration as well as for an improved understanding of the hydrologic mechanisms that affect salmonids in the region. migrants. Most (70%) hatchery origin adults were progeny of steelhead females. A significant fraction of progeny of both forms (34% and 38%) had adopted the opposite life history form of their mother. Natal signatures showed that 75% of hatchery origin adults reared in the MRFH as juveniles, 7% reared in the LMR, 1% were strays from Nimbus Hatchery, and 16% were transfers from Feather River Hatchery. Together, these findings suggest the natural origin population is a relatively closed population of non-anadromous forms, while the hatchery origin population exhibits high connectivity between forms.
Migratory histories, maternal origin, and connectivity of rainbow trout (Oncorhynchus mykiss) from the Lower Mokelumne River
Christopher J. Donohoe, Rachel Johnson, Peter K. Weber, Jose Setka, Severiano del Real
Institute of Marine Sciences, University of California, Santa Cruz, 100 Shaffer Road, Santa Cruz, CA 95060, (831) 2397911, cdonohoe@pmc.ucsc.edu
Bringing a river back to life

Elif Fehm-Sullivan
California Central Valley Office, 650 Capitol Mall, Suite 5-100, Sacramento, CA 95916, (916) 930 3723, elif.fehmsullivan@noaa.gov
The population dynamics of rainbow trout (Oncorhynchus mykiss) in the Lower Mokelumne River (LMR) depends on the relative abundance of the steelhead and non-anadromous life history forms, the rates of reproductive exchange between forms, and the connectivity to populations in other rivers in the Central Valley. However these data have been difficult to acquire using traditional approaches. We measured otolith 87Sr/86Sr ratios in natural origin and hatchery origin O. mykiss collected from the LMR and Mokelumne River Fish Hatchery (MRFH) from 20092012 to determine the migratory form, maternal origin, and natal origin (straying) of fish in the two populations. The natural origin population was dominated by non-anadromous forms; 3% of adults were steelhead and 97% were non-anadromous, with 81% resident in the LMR and 16% making freshwater migrations. Most (90%) adults were the progeny of non-anadromous females. Natal signatures showed that 89% of adults had reared in the LMR as juveniles, 7% reared in the MRFH (or possibly outside the LMR), and 4% were strays. In addition, 10% of parr and 15% of smolts were progeny of steelhead females. In contrast, the population of hatchery origin adults was mixed; 56% were steelhead and 44% were non-anadromous, with 9% resident in the LMR and 35% freshwater
This presentation offers a look at the San Joaquin river and the history associated with the San Joaquin River Restoration Program (SJRRP), including: how the program began, its goals, and how it has fostered collaboration between federal and state agencies, water users, farmers, land owners, environmental groups, engineers, and biologists.
Tuolumne, Stanislaus, and Yuba River floodplain versus flow relationships

Mark Gard
U.S. Fish and Wildlife Service, 2800 Cottage Way, Suite W2605, Sacramento, CA 95825, (916) 414-6589, mark_gard@fws.gov
A variety of techniques were used to quantify the relationship between streamflow and floodplain inundation area. For the Tuolumne River, an empirical method was used based on waters edge shapefiles digitized from aerial photographs of various flows. For the Stanislaus River, a two-dimensional hydraulic model was developed, using existing LIDAR and SONAR data, to predict the area of inundated floodplain at a range of flows. For the Yuba River, an existing two-dimensional hydraulic model was used to predict the area of inundated floodplain at a range of flows. The results of these studies can be used to develop instream flow recommendations for outmigrating anadromous salmonids and to prioritize areas for restoring/creating floodplain habitat.
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Collaboration and resource management in highly populated California
Tom Gohring
Executive Director Water Forum, 2831 G Street, Suite 100 Sacramento 95816
Quantifying existing Chinook salmon rearing and migration habitat for the San Joaquin River Restoration Program
Blair Greimann
Bureau of Reclamation, Denver Federal Center, Building 67, PO Box 25007, Denver CO 80225-0007, (303) 445-2563, BGreimann@usbr.gov
The combination of high population density, arid climate, and extensive cross-basin water development projects has resulted in increased environmental stressors, reduced habitat, and declining species populations in the California landscape. Associated reductions in water quantity and quality in California streams has led to conflicts over fishing, irrigation, development, water rights, and water project operations. Collaborative solutions, which often rely on interestbased, multi-party negotiations provide more durable solutions to these conflicts and ultimately provide greater resource protection. The Sacramento Water Forum will be used as an example to describe how collaboration among regulatory agencies, water managers, business interests and environmental groups has led to creative and lasting solutions to water-related conflicts on a river basin scale. Examples include exchange of information and integration of decisions across local, state and federal jurisdictions and technical disciplines.
Use of redd caps and egg tubes to asses spawning habitat of Chinook salmon
Jerrad Goodell
U.S. Fish and Wildlife Service, 850 S Guild Lodi, CA 95240, (209) 334-2968
The San Joaquin River Restoration Program (SJRRP)'s goals include restoring naturally reproducing and selfsustaining populations of salmon in the San Joaquin River between Friant Dam and the confluence with the Merced River. Long-term average population goals have been set at 30,000 returning adult spring-run Chinook salmon and 10,000 returning adult fall-run Chinook salmon, with fluctuations up to 45,000 springrun and 15,000 fall-run. The Emigrating Salmonid Habitat Estimation model quantified acres of rearing and migration habitat required for the offspring of these targets. Reclamation then used a two-dimensional hydraulic model and aerial photos to identify depth, velocity, and cover characteristics in each reach of the San Joaquin River. Habitat suitability indices were developed from nearby rivers with extant Chinook populations. Existing inundated areas were categorized by habitat suitability and summed by reach for representative flow levels. Existing suitable habitat varies substantially by reach. Physical limitations of the system, jointly operated for restoration and flood control, place limits on floodplain inundation and habitat effectiveness. Trade-offs and the opportunity for optimization exist between restoration and land acquisition costs. This talk will discuss the methodology, results, and implications for upcoming SJRRP projects.
The San Joaquin River Restoration Program has developed a series of small interdisciplinary groups (SIG) to focus on understanding and addressing life stage needs for salmon in the Restoration Area. The spawning gravel SIG has developed key questions surrounding the needs for the incubation / emergence life stage. This presentation will describe the current state of knowledge on incubation / emergence needs, discuss the relevant questions identified by the SIG and highlight an ongoing study being implemented to address some of these questions.
Trends in piscivory in an altered environment of the San Joaquin River

Kyle Griffiths, Steve Blumenshine
CSU Fresno, Department of Biology, 2555 East San Ramon Ave MS/73 , Fresno, California, 93740, (650) 219-0149. wgriffiths@csufresno.edu
Continuing water extraction and habitat loss have extirpated spring and fall runs of Chinook salmon from the San Joaquin south of the confluence with the Merced River. A comprehensive collaborative effort to restore both runs of Chinook to the San Joaquin is underway, including assessments of recruitment
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bottlenecks to out-migrating juvenile salmon, such as predation from assemblages of introduced piscivorous fishes. The U.S. Fish and Wildlife Service and the California Department of Fish and Wildlife sampled predatory fish assemblages in a potential predation gauntlet: a series of gravel mining pits in the river channel or connected by levee breaches. We estimated spatial and temporal variation in prey consumption rates of piscivores with bioenergetic models using diet sample data, estimated growth rates, and thermal history. Multivariate analyses and stable isotope ratios of C, N, and O were used to describe trends that could not be captured by point estimate snapshots (such as stomach contents). The majority of piscivore biomass was comprised of largemouth bass which exhibited a high dependence on crayfish, which was 60% of the consumed prey mass. Fish were frequently consumed but they were much less important energetically, comprising ~13% of all mass consumed. Preliminary results from 18O analysis indicate this isotope ratio may be useful to determine environmental history of sampled piscivores, and predict if fish movement patterns would spatially homogenize piscivory. A piscivory risk index was generated from the product of CPUE and fish consumption to aid prospective restoration actions such as physically separating highindex mine pits from the main river channel. upstream migration across a range of flow conditions. In the late summer and early fall of 2013, Branciforte Dam was removed. The project was lead by the Resource Conservation District of Santa Cruz County, with funding for coordination, feasibility assessment and design provided by the California Coastal Conservancy. The preliminary assessment and design were vetted through consultation with project partners including representatives from NOAA Fisheries, California Department of Fish and Wildlife, National Resource Conservation Service, Santa Cruz County, Santa Cruz County Resource Conservation District, Army Corps of Engineers, US Fish and Wildlife Service, and the Regional Water Quality Control Board. Following the assessment and development of an engineered design, the dam was removed with implementation funding provided by US Fish and Wildlife Service Fish Passage Forum, County of Santa Cruz, and American Rivers/NOAA. Details of the feasibility assessment, engineered design, construction and post-project monitoring will be discussed during the presentation.
Collaboratively improving salmonid spawning, rearing, and passage in Central Valley Project rivers
John Hannon
US Bureau of Reclamation, Bay Delta Office Science Division, 801 I Street, Suite 140 Sacramento, CA 95814, (916) 414-2413, jhannon@usbr.gov
Branciforte Dam Removal Project, Branciforte Creek, Santa Cruz, California

Chris Hammersmark, Ben Taber, Jim Robins, Kelli Camara
CBEC, Inc. Eco Engineering, 2544 Industrial Boulevard, West Sacramento, CA 95691 (916) 668-5236, c.hammersmark@cbecoeng.com
While dams provide several benefits towards mankind's occupation of the arid west (e.g., water supply, power generation, flood regulation, recreation, etc.), they also negatively impact physical and biological processes in river systems. Branciforte Dam was constructed on Branciforte Creek, a tributary to the San Lorenzo River, in 1931, for the purpose of water supply and recreation. The ~8 foot tall dam altered sediment movement downstream and fish passage to the ~3.5 square mile watershed located upstream, where high quality habitat exists. Multiple past attempts were made to retrofit the dam in order to provide and/or improve fish passage. However, the dam still posed an impediment to
Success of fish and habitat management activities depends largely on successful collaboration with local stakeholders early and often through an open and transparent dialogue conducted in a variety of settings. Landowners needs can usually be met by working together in one on one settings to identify common goals that will satisfy landowner concerns and result in a project benefitting landowners and the resources targeted for restoration. Community needs and concerns often run the gamut of potential opinions and need be addressed, or at least heard and acknowledged, in a variety of forums to meet the needs of individual stakeholders. Regulatory processes generally have a goal of protecting the very resources we are attempting to enhance so being mindful of that when collaborating with those responsible for implementing the regulations can reduce red tape. In a similar note, water operators can often help meet species needs, when those needs are known, within the extent of their flexibility. Project design,
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implementation, and monitoring that involve diverse stakeholders can foster continued success in future activities. Ill provide examples of successful and less than successful endeavors that strive to improve habitat and fisheries in Central Valley Project rivers. These include a continuing program to improve spawning and rearing habitats in the lower American, Sacramento, and Stanislaus rivers and an attempt to successfully provide salmonid passage around Shasta Dam.
Collaborative kernels: advances in the conservation and restoration of mountain meadows and streams in California
Rene Henery
Trout Unlimited of California, University of Nevada, Reno P.O. Box 3237, Santa Rosa, CA 95402-3237, (510) 528-4164, rhenery@tu.org
Low genetic diversity and reduced life history variation increase extinction risk within insular populations of an endangered fish
Michael Hellmair, Andrew P. Kinziger
FISHBIO, 180 E 4th Street, Chico, CA 95926. (707) 616-3820. michaelhellmair@fishbio.com
Loss of genetic diversity is considered detrimental to animal populations, yet the expressed fitness effects thereof are difficult to quantify in the wild. Theoretical work has shown that reduced phenotypic heterogeneity leads to population instability and increases extinction potential, yet few examples exist that illustrate how varying levels of genetic diversity may influence phenotypic variability in natural animal populations. In this study, we investigate the relationship between genetic diversity and life history variation among demographically independent populations of tidewater goby (Eucyclogobius newberryi) and propose that reductions in both factors contribute to extinction risk of these isolated populations. We illustrate that, for this annual species, continuous reproduction is a safeguard against reproductive failure by any one population segment, as natural, stochastically driven salinity increases frequently result in high mortality among juvenile individuals. Populations with low genetic diversity exhibit truncated reproductive periods, rendering them vulnerable to extinction in the event of environmental fluctuation. In contrast, continuous presence of adults with broader physiological tolerance to abrupt salinity changes allows genetically diverse populations to persist through such periods. These findings assert the importance of maintaining healthy levels of genetic- and life history variation, and warrant the consideration of genetic supplementation as a management tool for in the quest for conservation of this species
Sierra Nevada mountain stream-meadow complexes provide a broad range of beneficial services including water filtration, water storage, lower summer stream temperatures, and critical habitat for many different species. This range of benefits, coupled with Californias complex landscape has led to a diverse array of mountain meadow and stream enhancement approaches being applied across California, as well as an equally diverse and often poorly defined accompanying suite of recovery goals and objectives. As a result is has often been difficult to measure the success of restoration actions both at the individual project and landscape scales, or to effectively prioritize future actions or adaptive management. Over the last several years, with support from the NFWF Sierra Nevada Meadow Restoration Program, Trout Unlimited (TU) has partnered with state and federal agencies, NGOs, Universities and private landowners to refine the development, prioritization, execution, and maintenance of mountain stream and meadow enhancement efforts across California. Some specific focus areas have included a) framing a process based approach to mountain stream-meadow conservation planning, b) developing physical habitat recovery targets to support fish recovery objectives, c) quantifying restoration effects at the habitat scale, as a measure of restoration success, and d) prioritizing additional enhancements or adaptive management actions for maximum benefit to target aquatic species. This presentation will provide an overview of progress made in these topic areas including specific examples, details about design and application, early successes, and lessons learned.
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Dont need a mate, just need a trout: genetic and demographic structure of three western pearlshell mussel (Margaritifera falcata) populations in the western Great Basin
Chris Hogle, Veronica Kirchoff, Mary Peacock, and Don Sada
Desert Research Institute (University of Nevada, Reno) 2215 Raggio Pkwy. Reno, NV 89512, (530) 902-5972, chris.hogle@dri.edu
Western pearlshell mussels ( Margaritifera falcata) are facultative hermaphrodites characterized by their longevity and need for cold, clean streams and healthy salmonid host populations. Microsatellites and lengthfrequency analyses were used to relate multi-decade demographic and genetic trends in three M. falcata populations in the western Great Basin. Long-term trends in allele frequency and heterozygosity indicated high levels of inbreeding and frequent self-fertilization even in demographically healthy populations. Inbreeding has led to the fixation of alleles and divergence between isolated populations. Other populations exhibited genetic similarity due to historic connectivity provided by a migratory host population. The presence of healthy populations characterized by naturally high inbreeding rates indicates some populations of M. falcata may be resistant to inbreeding depression.
(USFWS) Anadromous Fish Restoration Program (AFRP), under the federal Central Valley Project Improvement Act (CVPIA), was charged with making all reasonable efforts to at least double natural production of six anadromous species on a sustainable basis and has identified 172 actions to help meet this goal. The AFRP approach to make all reasonable efforts to meet this lofty assignment requires partnerships, local involvement, public support, adaptive management, and flexibility. The Program has embraced the fact that public support is both a product and a prerequisite of successful partnerships and local involvement. Since its inception, the Program has achieved notable successes and met numerous challenges. During this presentation, I will discuss collaborative efforts by AFRP with partnering agencies, resource managers, and fisheries and physical scientists to manage and rehabilitate valuable freshwater resources within the challenging environment of the California Central Valley.
Using DIDSON during turbid water periods to compliment overhead and underwater video to estimate Chinook salmon escapement in tributaries of the Upper Sacramento River
Matthew R. Johnson
California Department of Fish and Wildlife, 1530 Schwab St., Red Bluff, CA 96080, (530) 527-8893, Matt.Johnson@wildlife.ca.gov
Doubling anadromous salmonid and sturgeon populations in the California Central Valley; twenty-five years of challenges and success
Zachary Jackson
US Fish and Wildlife Service, AFRP 4001 N. Wilson Way Stockton, CA, CA 95205, (209) 334-2968 x408, zachary_jackson@fws.gov
Over the past 180 years anthropogenic effects including mining, flood protection, power generation, water development, stream and floodplain conversion, water quality degradation, invasive species, harvest, and hatchery managementhave stressed, altered, and depleted native anadromous fishes including Chinook salmon, steelhead, and white and green sturgeon. Global parameters, such as ocean conditions, have also demonstrated a marked effect on several species. In 1998, the United States Fish and Wildlife Service
The California Department of Fish and Wildlifes Red Bluff Fisheries Office currently operates and maintains video stations on Battle, Cow, Cottonwood, Clear, Antelope, and Mill Creeks for the purpose of obtaining Chinook salmon population estimates. Since large Cyprinids are frequently encountered at Upper Sacramento tributary video station sites as residents, or during the process of undergoing their own spawning migrations, video imagery has proven to be the most effective means of obtaining accurate salmon counts where these species overlap in fork length and swimming behavior. These video stations employ an overhead video camera trained on a contrasting while plate anchored to the stream bottom at a weir opening or fishway exit. Additional underwater cameras are strategically placed within the weir or fishway opening to provide broadside images of fish for identification. However, when significant increases in turbidity following high water or snow melt events occur usable video images are not obtainable for hours or days at a
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time. During these periods deployment of a DIDSON unit at the weir or fishway opening takes the place of video cameras, and this strategy has proven to be an invaluable method for maintaining continuous recording of fish passage events and obtaining accurate population estimates. Using DIDSON alone, without underwater video camera verification of targets 610 mm or larger, has proven very problematic in the lower reaches of Upper Sacramento River tributaries, as evidenced by a study completed on lower Deer Creek, Tehama County in spring of 2013. trash rack mostly left (1 as far as Red Bluff on the upper Sacramento River).
Klamath River: out of the box FERC relicensing

Curtis A. Knight
California Trout, 701 S. Mt. Shasta Blvd., Mt. Shasta, CA 96067, 530-859-1872, cknight@caltrout.org
Summary of 2013 juvenile salmonid acoustic telemetry behavior study at the Bureau of Reclamation Tracy Fish Collection Facility
Cathy Karp, Brandon Wu
Bureau of Reclamation Denver Technical Services Center, PO Box 25007, Denver, CO 80225-0007, (303) 445-2226, ckarp@usbr.gov
In spring 2013, we released acoustically tagged juvenile Chinook salmon (n=69, 136.2 mm mean fork length, late-fall run Coleman National Fish Hatchery), juvenile steelhead (n=64, 198.7 mm mean fork length, Mokelumne River Fish Hatchery), and adult striped bass (n=36, 510 mm mean fork length, collected by angling and predator removals) at the Bureau of Reclamations Tracy Fish Collection Facility, Tracy, CA, to begin to quantify fish losses to predation and facility structure (louver/bypasses). A system of 21 acoustic telemetry hydrophones were set up upstream, within, and downstream of the fish facility. Fish were released over a 3 day experimental period in March and May. Flow conditions ranged from 0.6 to 2.9 fps in the primary channel and 2.5 to 2.8 fps in the secondary channel (flows were highest on day 1, intermediate on day 2 and lowest on day 3), beginning at 7am each day for 24 h. Fish releases were conducted during both day and night conditions (8am, 11am, 2pm, 8pm, 11pm, 2am for salmonids; 8am, 4pm, 12am for striped bass) during each 24 h flow condition. A total of 37 tagged salmonids (28 Chinook salmon, 9 steelhead) were recovered in the holding tanks and exhibited a wide range of behavior. Twenty-nine fish were lost to predation and louvers (24 Chinook salmon, 5 steelhead). Acoustic telemetry data for the remaining fish are still being analyzed for the time following each 24 study period and include fate categories of swim-out and non-participation. The striped bass released into the facility remained while those released in front of the
The Klamath River provides an informative case study for how a FERC relicensing process can facilitate and leverage a broader watershed wide agreement. In 2000, PacifiCorp initiated the FERC #2082 relicensing proceeding for 5 dams on the Klamath River. This talk will focus on the Klamath River FERC proceeding and how the process eventually evolved into the creation of two settlement agreementsKlamath Basin Restoration Agreement and the Klamath Hydroelectric Settlement Agreement (Klamath Agreements). I will focus on a several events and FERC policies that contributed to the final outcome of the relicensing proceeding. A few of these include a near complete shut-off of irrigation water in the upper basin in 2001 and in the following year a fish kill in the lower river that left over 33,000 salmon dead. Another large influence in the proceeding was the Energy Policy Act of 2005 which allowed the utility (or any other party) to challenge federal agency authority under Sections 4(e) and Section 18 of the Federal Power Act. PacifiCorp utilized this option shortly after the Act was issued resulting in one of the first trial type hearings of its kind. The FERC proceeding was a precursor to the development of comprehensive, basin wide settlement agreements on Klamath River. The proceeding brought parties together creating new partnerships, a forum for reviewing data about the river and the dams, and set the stage for collaborative solutions. By 2006 the FERC proceeding had shifted to settlement talks and in 2010 the Klamath Agreements were signed by 42 parties including tribes, agencies, conservation groups, commercial fisherman, water users, and PacifiCorp. The Agreements provide for basin wide water allocations and management, habitat restoration, provisions for community sustainability and the removal of 4 dams by 2020.
Declining downstream: modeling efforts to assess recruitment to frog populations in Californias regulated rivers
Scott McBain, Sarah Kupferberg
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McBain & Associates, 980 7th Street, Arcata, CA 95518, (510) 367-4546, skupferberg@gmail.com
The river breeding foothill yellow legged frog ( Rana boylii), is in decline downstream of large dams. Several physically-based factors influenced by upstream dam operations (and natural hydrology) may impair its ability to recruit new individuals to its populations. These include: current velocity and stage changes during egg incubation that result in desiccation or scour; reduced water temperatures in spring due to hypolimnetic releases that slow embryonic development and thus extend the period of desiccation / scour risk; and cool summer temperatures that decrease survival, decrease size, and increase time to metamorphosis. To inform flow management that can reduce these mortality agents, we developed a spreadsheet model to predict the hydrologic and thermal mechanics of breeding timing, embryonic and larval development. The model integrates knowledge of individual ecophysiological and behavioral responses to water temperature with channel morphology and stage discharge relationships. When applied to three different regulated rivers in California where dams release cold water from the depths of the upstream reservoir (Trinity, Tuolumne, and Alameda Creek) we found that the effects of cooler summer temperatures on tadpoles may have more profound impacts than the effects of spring flow fluctuation on clutches of eggs. To assess the spatial extent of thermal impacts of dam operations on frog populations, we combined knowledge of tadpole thermal preference and performance with temperature models forecasting the warming of water as it travels downstream from point of release. These techniques could be applied to other warm-water adapted ectothermic taxa when evaluating alternative flow proposals during FERC re-licensing of hydroelectric dams.
Northern DPS (the former a threatened species and the later a species of concern under the U.S. Endangered Species Act). Adult fish from these two DPS, can be found in the near-shore and coastal estuaries of Oregon, Washington and British Columbia, when not spawning in their natal streams in northern California and southern Oregon. They are most readily apparent and susceptible to capture during their summer-time aggregations in the major coastal estuaries (such as Grays Harbor, Willapa Bay, and the Columbia River estuary). Through collaborative efforts, state and federal researchers have been able to greatly expand their understanding of the species. Migration patterns, foraging behavior, population structure, and potential exposure to toxins have been some of the areas explored.
Use of dual frequency identification Sonar (DIDSON) to monitor steelhead escapement in the Smith River, California
Zachary S. Larson
Zach Larson and Associates, 200 Douglas Park Dr., Crescent City, CA 95531, (707) 954-1085, zach_larson@yahoo.com
Green Sturgeon Research in the Washington and Oregon Coastal Estuaries

Olaf P. Langness, Phillp E. Dionne, Chris Wagemann
Washington Department of Fish and Wildlife, 2108 Grand Blvd., Vancouver, WA 98661. (360) 606-7398. olaf.langness@dfw.wa.gov
The North American green sturgeon (Acipenser medirostris) population consists of two distinct population segments (DPS)the Southern DPS, and the
Long Range Dual Frequency Identification Sonar (DIDSON) was used to quantify adult fish passage 24 hours per day during the winter steelhead run-time in the Smith River, Del Norte County, California. Two long range DIDSON units operated continuously at river mile 6 for 108 consecutive days from 14 Dec 2012 to 31 Mar 2013. The number of adult fish counted passing upstream was 9,562 fish and 784 adult fish were counted passing downstream. A 20 minute per hour sampling rate was applied to the entire data set and the percent error for the season was less than 2 percent. Percent error was highest during March (24 percent) lowest during February (0.1 percent), indicating that results of studies with reduced sampling rates may be affected during kelt migrations. A high resolution lens fitted to the left bank DIDSON improved the image quality of fish at greater ranges and reduced positive bias in fish length measurements. Fish lengths averaged 74 cm during the study. Data were compared to weir counts at Rowdy Creek, a Smith River tributary located 2 miles downstream from the DIDSON station, and spikes of upstream fish passage at the DIDSON station coincided with peak steelhead counts at Rowdy Creek. This study provides the third consecutive year of time series DIDSON data for the Smith River during the
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winter steelhead run for helping to assess steelhead status and trends.
Ecosystem response to spawning bed enhancement in Deer Creek, Yuba River tributary
Justin Wood, Jeff Lauder
Sierra Streams Institute, 431 Uren Street Suite C Nevada City, CA 95959, (530) 265-6090 x204, justin@sierrastreams.org
Investigations into Hardhead (Mylopharodon conocephalus) life history in the San Joaquin drainage
Wayne Lifton, T. Earl Gonsolin, Robert Stoddard
Cardno ENTRIX 2300 Clayton Rd Suite 200, Concord, CA 94520, (925) 935-9920, wayne.lifton@cardno.com
Deer Creek flows for thirty-four miles in the Sierra Nevada foothills to its confluence with the lower Yuba River. As the last tributary of the Yuba River before the impassable Englebright Dam, Deer Creek provides habitat for Central Valley Chinook salmon and Steelhead. There is a lack of suitable spawning materials in Deer Creek due to the presence of upstream dams. Since 2010, Sierra Streams Institute (SSI) has been undertaking projects to augment the supply of spawning material in Deer Creek, including spawning bed enhancement efforts in 2012 and 2013. To evaluate how the spawning materials are incorporated into the aquatic system, we monitored benthic macroinvertebrates and algae, Chinook salmon and steelhead, water quality, and habitat conditions in three enhanced and three unenhanced areas. We also monitored mammalian and avian visitation to gauge ecosystem response. Pebble counts and bulk sediment samples indicate the median pebble size (d50) in each of the enhanced areas was reduced to a size suitable for salmon spawning. In both years over 75% of spawning activity occurred in enhanced sites, with three times more salmon redds in 2012 than 2011, and five times more in 2013 than 2011. Mammal surveys revealed an impact on trophic interactions as a result of increased salmon activity. We found no significant difference in benthic communities between modified and unmodified sites by week 4 (p<0.05), and no significant difference in algae cover by week 10. Sorenson distance between modified and unmodified sites decreased to <0.5 by week 8. 75% of food source macroinvertebrates sampled were more abundant in modified sites (p<0.05). The data suggest that the streams spawning capacity had been limited by lack of suitable habitat materials, spawning gravels can be quickly incorporated into the aquatic system by benthic organisms, and spawning bed enhancement can elicit an ecosystemwide response.
Monitoring of native fish species in the Horseshoe Bend Reach of the San Joaquin River has been conducted periodically over the past 30 years. Over the past eight years, detailed studies of native fish, especially hardhead (Mylopharodon conocephalus) have taken place as part of the implementation of a native aquatic species management plan to conserve and protect native species. These studies have focused on aspects of hardhead life history and habitat use. Techniques have involved radio tracking, larval trapping and netting, snorkel surveys, quantitative electrofishing, and visual observations. Data collected provided valuable insight into hardhead spawning behavior, responses to high flows, and habitat use. Hardhead adults were found to have fidelity to their habitats for rearing and spawning. There was limited indication of movement beyond a few habitat units for most adults. Spawning was observed to occur generally within those same habitats. The effect of high flows on movement and recruitment were also evaluated with decreased recruitment of young of the year found in high flow years.
Important factors influencing predatory fish mercury concentrations in California Reservoirs: a statistical approach
Stephen Louie
Central Valley Regional Water Quality Control Board, 11020 Sun Center Drive, Suite 200, Rancho Cordova, CA 95670-6114, (916) 464-4627, Stephen.Louie@waterboards.ca.gov
Mercury is negatively impacting many waters in California. Currently, about 75 lakes and reservoirs are officially designated as impaired by mercury because they have fish mercury concentrations that pose risks to human and wildlife consumers. Fish mercury levels are elevated in about half of all California lakes and reservoirs sampled. In addition, the California Office of Environmental Health Hazard Assessment has issued many advisories for limited or no consumption of many popular sport fish in California lakes and reservoirs. The
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inability to safely consume fish from many California lakes and reservoirs devalues California fisheries as a food source for humans and wildlife. Mercury impairment is due to several interrelated factors: inorganic mercury sources; conditions in reservoirs that cause the conversion of inorganic mercury to methylmercury and its subsequent bioaccumulation in the food web; and fish species present. This is one of two presentations on the State Water Boards development of a Statewide Mercury Control Program for Reservoirs. The project involves: identifying mercury sources to reservoirs; evaluating reservoir, watershed, and fisheries conditions; determining the linkage between reservoir fish mercury levels, reservoir and watershed conditions, and mercury sources; and identifying controllable factors that determine reservoir fish mercury levels. These analyses build on the robust scientific foundation previously developed for mercury total maximum daily loads in California. Potential solutions to reduce fish mercury concentrations include: mercury source controls, reservoir water chemistry management, and fisheries management. Water Board staff will present the statistical models we developed that explain reservoir fish tissue concentrations in 350 mm bass. The models explaining the greatest variability in fish mercury concentrations included chlorophyll-a, annual water level fluctuations, and mercury concentrations in sediment or water. Together, these variables explain 60-80% of the variability in fish mercury concentrations. Other important factors include: reservoir characteristics, land uses, and atmospheric mercury deposition. and what often goes wrong in collaboration on watershed or species recovery plans. By relating watershed-wide planning efforts to Maslows Hierarchy of Needs, we can begin to understand why the general public and politicians sometime seem less than enthusiastic about funding such efforts. Fear of loss or deprivation is at the heart of what motivates us. The trick is to communicate what will be lost by not achieving recovery or restoration.
Fish friendly farming: collaborative restoration and management

Laurel Marcus
CA Land Stewardship Institute, 550 Gateway Dr #108 Napa, CA 94558, laurelm@fishfriendlyfarming.org
Using the F-Word: FISH

Carol Mahoney
Zone 7 Water Agency, 100 N. Canyons Pkwy Livermore, CA 94551, (925) 454-5064, cmahoney@zone7water.com
The Fish Friendly Farming Program provides a sciencebased assessment and farm conservation plan for agricultural and ranch lands. Each plan covers the entire property not just the irrigated area and is comprehensive in scope including roads assessments, water supply and water rights review and conservation measures, erosion control and an assessment of the entire creek network. Currently there are over 130,000 acres in the program in California. The certification is completed by agencies and focuses on water quality and stream habitat improvements. After 5 years a recertification is done. The program is popular and considered to provide compliance with water quality regulatory programs such as TMDLs and waste discharge requirements (WDRs) for agriculture. A number of larger projects have developed from the program where there are a number of certified sites along a river or creek or where a particular problem is found in a region and needs a solution. Several examples of these collaborative restoration projects done with private landowners will be presented.
Merced River Ranch: collaboration on a science-based, community-driven restoration project

Joseph E. Merz
Cramer Fish Sciences. 3300 Industrial Blvd, West Sacramento, CA 95691, (209) 847-7786, jmerz@fishsciences.net
Why is there sometimes public resistance to large-scale recovery plans or watershed plans? How can we meet needs of threatened and endangered species while achieving positive political will? Does economic development and species preservation have to be on opposite sides, and if not, why does is always seem to be the case? The discussion Using the F Word: FISH focuses on the psychology of watershed planning
The Merced River Ranch Restoration Project is almost 20 years in the making. At construction completion, impacted channels, banks and floodplains from gold
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mining along the legendary Merced River, California, have been transformed into nearly six acres of seasonal salmonid rearing habitat and upland oak-grassland habitat and four acres of restored in channel spawning and rearing habitat. As envisioned, targeted Chinook salmon and steelhead have demonstrated use of the site, along with numerous other native aquatic and terrestrial plant and animal species. This project has also provided powerful educational opportunities for local school children, university graduates, and supported other public benefits. However, the entire process required an overall vision and significant collaboration among landowners, water purveyors, local communities, private and public scientists and engineers, construction teams, and numerous resource agencies. I will discuss the general history behind the site and convey the outreach, regulatory, development, monitoring and construction steps taken to see this project to completion.
Assessing the effects on fishes from pile driving sound Exposure: application of interim hydroacoustic criteria
Jacqueline Pearson Meyer
NOAAs National Marine Fisheries Service West Coast Region, California Coastal Area Office Santa Rosa, CA 95401, (707) 575-6057, jacqueline.pearson-meyer@noaa.gov
Using DIDSON in life cycle monitoring on Redwood Creek, Humboldt County

Mathew Metheny, Walter Duffy, Michael Sparkman
California Cooperative Fish and Wildlife Research Unit, Humboldt State University, Arcata, California 95521, (707) 826-3268, wduffy47@gmail.com
We have been operating a DIDSON camera as part of a life cycle monitoring station on Redwood Creek in Humboldt County. This watershed was originally selected as a pilot for a DIDSON deployment because it presents multiple challenges. Redwood Creek supports four species of anadromous salmonids, it is the median size river in the SONCC coho salmon ESU, its discharge is flashy, and the river is often turbid and has an unstable bed, the result of legacy logging practices. Despite these challenges, this DIDSON camera has provided escapement estimates in all but one year. WE use logistic regression informed by live fish observations and run timing to assign species and here discuss escapement estimates for Chinook salmon, coho salmon and steelhead for the several migration seasons as well as sources of error. We also discuss these DIDSON results in the context of the coastal salmonid monitoring plan and compare results with those from redd surveys.
NOAAs National Marine Fisheries Service (NOAA Fisheries) works to conserve, protect, and recover marine species, including anadromous fishes protected under the Endangered Species Act (ESA), and/or the essential fish habitat provisions of the MagnusonStevens Fishery Conservation and Management Act (MSA). Protected fish species may be injured or killed from exposure to the underwater sound produced during impact pile driving. Therefore, NOAA Fisheries works collaboratively with other federal, state, local government and nongovernmental agencies, academia, and industry to best assess and manage risk to fishes from these activities. The Fisheries Hydroacoustic Working Group (FHWG) is a cooperative effort between federal and state transportation and resource agencies along the west coast of the United States. The FHWG has established interim hydroacoustic criteria for the onset of injury to fishes exposed to the underwater sounds generated by impact pile driving. NOAA Fisheries uses these criteria to assess potential impacts to protected fish species during consultation with federal agencies on projects that include pile driving in, or near, aquatic environments. The criteria use two metrics peak sound pressure level (SPL) and sound exposure level (SEL). The onset of physical injury would be expected if either the peak SPL exceeds 206 dB (re: 1 Pa) or the daily cumulative SEL exceeds 187 dB (re: 1 Pa2sec) for fishes 2 grams or larger, or 183 dB for smaller fishes. Here I will present these criteria and how we use them to assess the risk to fishes that are listed under the ESA or the essential fish habitat managed under the MSA.
Seasonal distribution of green and white sturgeon in the San Francisco Bay, Delta, and Sacramento River
Emily Miller, Michael Thomas, Gabe Singer, Matthew Peterson, Eric Chapman, Ryan Battleson
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University of California, Davis Department of Wildlife, Fish, and Conservation Biology One Shields Avenue, Davis, CA 95616, (530) 752-3203, eamiller@ucdavis.edu
Restoration can lead to innovation: The SJRRPs Arroyo Canal Fish Screen and Sack Dam Fish Passage Project
Leslie Mirise
California Central Valley Office, 650 Capitol Mall, Suite 5-100, Sacramento, CA 95916, (916) 930-3638, leslie.mirise@noaa.gov
Green and White Sturgeon are large, long-lived, sympatric sister taxa found in the San Francisco Bay, Sacramento-San Joaquin Delta, and Sacramento River watershed. Green Sturgeon are listed as threatened while White Sturgeon are more abundant, though they too are vulnerable to declines in part due to their highly variable annual recruitment. Though similar, the two species' life history strategies differ in several ways including their geographic distributions and migration patterns. Understanding how the Green and White Sturgeon partition their niche space with different seasonal distributions has the potential to inform management decisions. We surgically implanted coded acoustic transmitters in sturgeon which were then detected by an array of over 300 stationary acoustic monitors throughout the watershed. Mean river kilometer differed between Green and White Sturgeon at all size-classes and had greater divergence at larger size-classes. Additionally, we modeled the likelihood of the presence of each species by reach within the watershed throughout the year. This study examines niche overlap by reporting sturgeon seasonal distributions as well as notes on life history stages.
How the advancement in field data collection devices can help you get more work done in less time with better results
Shaun Minton
Electronic Data Solutions Territory Manager, 2423 Barona Street, West Sacramento, CA 95691, (916) 601-6703, shaun@elecdata.com
The San Joaquin River Restoration Program (SJRRP) will reintroduce an experimental population of spring-run Chinook salmon to the upper portion of the San Joaquin River above the confluence with the Merced River upstream to Friant Dam, known as the SJRRP Restoration Area. The Arroyo Canal and Sack Dam (which creates backwater to feed Arroyo Canal) are located in a central portion of this Restoration Area. Currently, passage is not available at Sack Dam except during high flood flows, and the diversion at Arroyo Canal is unscreened. The Settlement requires infrastructure improvements at both locations to improve fish habitat conditions with a focus on Chinook salmon. Proposed improvements include an off-channel fish screen at Arroyo Canal and innovative passage designs at Sack Dam in order to pass multiple fish species, including sturgeon. These improvements aim to meet the Settlements dual goals to maintain fish populations below Friant Dam in good condition and reduce or avoid adverse water supply impacts to Friant Division long-term contractors. This talk will focus on the experimental nature of the fish passage structure as it incorporates innovative designs. A series of options will be available for upstream and downstream migrating fish depending on flow rate. Monitoring will be performed to assess the effectiveness of these passage options.
High accuracy GPS that works under trees, software that utilizes the latest mobile devices and smaller and lighter field collection equipment all equal a better work flow for people whose jobs require them to collect data in remote locations. This talk will focus on the very latest in technologies that just a couple of years ago would not have existed. If you are a field professional who wants to make use of sub-meter GPS collection devices that can be dropped in streams and rivers and even have the ability to send your data back to the office in real time, this presentation will show just what the new field solutions are capable of.
Pile Driving on Large Bridge Projects in CA; Case Studies of Aquatic Species Impacts and Attenuation Methodology
Melinda Molnar
California Department of Transportation, 1656 Union Street Eureka, CA 95001, (707) 445-6627, Melinda_Molnar@dot.ca.gov
In October 2000, Caltrans started driving test piles for the San Francisco-Oakland Bay Bridge, seismic safety project. Underwater noise pressure waves radiated from the impact driving activity, resulting in mortality to
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fish. At that time, Caltrans, the National Marine Fisheries Service (NMFS), and the U.S. Fish and Wildlife Service (U.S. FWS), realized the need to address potential hydroacoustic impacts to fish and other aquatic species, related to pile driving activities. Due to the need to develop information and research on effects criteria for fish, in 2004, Caltrans in coordination with Washington DOT, Oregon DOT, Federal Highways Administration (FHWA), NMFS, California Department of Fish & Wildlife (CDFW) & U.S. FWS, established the Fisheries Hydroacoustic Working Group (FHWG). In June 2008, the FHWG agreed on both peak and accumulative thresholds for fish exposed to pile driving operations. This presentation chronicles recent scientific and engineering advancements regarding hydroacoustic impacts to fish and other aquatic species, on large bridge projects such as the San Francisco-Oakland Bay Bridge, the Humboldt Bay Bridges, Mad River Bridge, Van Duzen River Bridge and the Confusion Hill Bypass (Eel River). It further provides information on hydroacoustic impact findings, pile driving methodologies, available underwater noise attenuation devices, current and ongoing research as well as multiple-agency threshold agreements. Rogue River, Oregon, we compared this new method to traditional mark-recapture sampling and found that the DIDSON transect technique required fewer technician hours to perform and resulted in superior confidence intervals bounding the estimate of the number of sturgeon present. During the summers of 2010-2012 we applied this method within all three rivers known to support Green Sturgeon spawning and identified consistent patterns of spawning habitat utilization. We then estimated the total number of annually spawning individuals in each population. The DIDSON transect technique has greatly informed the recovery planning for this imperiled species and is likely of great utility to other large bodied anadromous fish species.
Timelines and deadlines: aligning settlement deadlines, project schedules, and salmon reintroduction on the San Joaquin River
John Netto
San Joaquin River Restoration Program Coordinator, U.S. Fish and Wildlife Service, 2800 Cottage Way, Sacramento, CA 95825, (916) 978-5459, John_Netto@fws.gov
Estimating the abundance and distribution of spawning Green Sturgeon using a DIDSON acoustic camera
Ethan Mora
UC Davis, Department of Wildlife, Fish and Conservation Biology. UC Davis 1134 Academic Surge Building, Davis California 95616, (714) 642-6559, eamora@ucdavis.edu
Data describing the annual run size and habitat occupancy of spawning Green Sturgeon have been difficult to obtain. Previous methods to determine these characteristics have been based on either markrecapture studies that are invasive and time consuming, or acoustic/radio telemetry studies with potentially biased estimates due to small sample sizes. We present an efficient, non-invasive method to identify the abundance and distribution Green Sturgeon during their spawning period. Using a Dual Frequency Identification Sonar (DIDSON) we are able to sample riverine habitat for the presence-absence of Green Sturgeon and combined with transect based sampling techniques, estimate the abundance of spawning adults. In the
The Stipulation of Settlement and San Joaquin River Restoration Act specify a number of actions, requirements, and deadlines for restoring the San Joaquin River above the confluence with the Merced River and initiating the reintroduction of Fall-run and Spring-run Chinook Salmon. The process for design, planning, and compliance is taking longer than was envisioned in the Settlement; the construction projects are several years from completion, and we are still working towards having flow connectivity through the Restoration Area. Completion of the projects will ultimately be necessary to meet the Restoration Goal of establishing self-sustaining populations of Chinook salmon and other fish. Prior to the completion of these projects, the Program will further progress towards the Restoration Goal, and has initiated of number of fishery actions to inform the program and jumps start the process for establishing of salmon populations in the river. As the schedule for completion of the construction projects become clearer, so will the targets and timeline for salmon reintroduction.
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Physiological effects of boat noise on a coastal marine fish, the Giant Kelpfish, Heterostichus rostratus.
Tye Nichols
San Diego State University, Department of Biology, 5500 Campanile Dr, San Diego, CA 92182, (916) 709-4221, tyenichs@gmail.com
Boat engine noise is the most common form of noise pollution in marine environments, yet its effects on marine organisms are poorly understood. Here we investigate the stress response of a coastal fish, the giant kelpfish (Heterostichus rostratus), to boat noise with different temporal patterns and intensities. Juvenile fish were exposed to three types of boat noise in laboratory aquaria: continuous, regular intermittent and random intermittent. Cortisol concentrations were measured and compared to those of fish exposed to continuous natural ambient sound. The random intermittent treatment elicited the highest cortisol levels of all treatments. To determine how noise intensity and distance from a noise source may influence the stress response, fish in aquaria were exposed to random intermittent boat noise recorded at a range of distances from the boat engine. Cortisol concentrations exhibited a non-linear decrease with increasing distance of the recording, dropping markedly in response to recordings made at greater distances. This is the first study of which we are aware to demonstrate that the temporal pattern of a noise stressor is an important determinant of a stress response. These results also suggest that small differences in distance from the noise source may cause large differences in the stress response.
represent attributes of systems or populations using as small of a sampling as possible and thus can be highly economical and tractable. However, statistics cannot address organized spatial and temporal patterns that are essential for understanding and predicting physical mechanisms and ecological functions. They also cannot cope with important, rare phenomena that are difficult to sample according to statistical norms. Further, in the adversarial, litigious social process of FERC relicensing, it is very easy for opponents of any statistical analysis to demonstrate its invalidity. In turn, a lot of money is spent on meetings for aggressive negotiations over topics for which there exists no local scientific analyses. At some point, applied science needs to move beyond statistical sampling and into census-based sampling and analysis. Near-census river science is a comprehensive, spatially explicit, process-based paradigm for studying rivers emphasizing the 1-m scale as the basic building block for characterizing geomorphic processes and ecological functions. By eliminating all the decisions that go into sample selection upfront, it is possible to analyze the totality of a landscape in fine detail with no compromises. There is still a lot to argue about in the FERC social process, but at least the topic of sampling design is removed and exciting new spatial perspectives are brought in. Finally, whereas statistics can only be used for analysis, near-census methods also provide required tools needed for redesigning flow regimes and river landforms. This presentation will illustrate some of the latest tools and applications of near-census river science in FERC relicensing on the Yuba River, California.
Plasticity of breeding in foothill yellow-legged frog (Rana boylii) in the Sierra Nevada: best monitoring practices
Ryan A. Peek, Sarah M. Yarnell
Center for Watershed Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, (530) 754-5351, rapeek@ucdavis.edu
Use of near-census river science to avoid conflicts in FERC relicensing due to statistical sampling ambiguity
Gregory B. Pasternack
Department of Land, Air, and Water Resources 223 Veihmeyer Hall, University of California at Davis, Davis, CA 95616, (530) 302-5658, gpast@ucdavis.edu
During the 20th century, statistical sampling and analysis came to dominate environmental science and management, because it yields quantifiable metrics and performance indicators. Statistics aims to accurately
Variability in ecosystems provides heterogeneity through time and space, and organisms in stochastic systems such as rivers must evolve physiological or life history adaptations that allow flexible responses to seasonal and annual variability. This biological plasticity may be tied to environmental cues that forecast stable conditions suitable for sensitive life history stages. The lotic Rana boylii (foothill yellow-legged frog) breeds in very similar hydrologic conditions across watersheds and years, despite a highly variable geographical and
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environmental gradient across its range from southern Oregon to northern Baja California. We suggest R.boylii utilize specific environmental cues (flow recession rate and water temperature) to project the onset of suitable and stable hydraulic and thermal periods for initiation of spring egg deposition (oviposition) because these signals remain consistent across spatial and temporal scales. We compare and analyze R. boylii breeding data in conjunction with flow recession rates and water temperature to demonstrate differences in inter-annual breeding timing between wet years and dry years. Rana boylii shows high plasticity in the timing of breeding, but remains strongly correlated with hydrological cues such as the rate of the natural spring snowmelt recession in the Sierra Nevada (approximately 10 cm per week) and 7-day mean weekly water temperatures that exceed 10 C. Summary of over 10 years of breeding data for R. boylii across California shows the range in breeding timing can vary by 4 months, from early March to early July. In addition, egg mass water depth can also be highly variable, with observations ranging from <0.2 m to over 2 m over 5 years at one site. Because of the range of natural variability in both timing and microhabitat use, we suggest a revised monitoring survey protocol for frogs that improves potential breeding detections to better optimize limited resources within the FERC monitoring framework. (Acipenser medirostris) have been shown to have high entrainment rates into unscreened diversions in the laboratory, and do not display effective avoidance responses. Therefore we tested the efficacy of a sensory deterrent (strobe light) and two structural pipe modifications (upturned pipe configuration, altered pipe plate) in reducing the entrainment of juvenile green sturgeon (mean mass = 167.1 4.0 g; mean fork length = 31.9 0.3 cm) in a large (>500 kL) outdoor flume fitted with a 0.46m diameter water diversion pipe. The upturned pipe and altered pipe plate modifications significantly reduced fish entrainment rates relative to control (1.6 0.5% vs. 25.5 3.2% and 5.7 0.7% vs. 25.5 3.2%, respectively), while the presence of the strobe light did not affect fish entrainment rates. These data suggest that sensory deterrents are not an effective means to reduce diversion pipe interactions for green sturgeon, but that structural alterations to diversions can successfully reduce entrainment for this species. Our results are informative in developing effective management strategies to mitigate the impacts of water diversions on sturgeon populations, and suggest that effective restoration strategies that balance agricultural needs with conservation programs are possible.
The efficacy of deterrents and pipe modifications in reducing entrainment of juvenile green sturgeon (Acipenser medirostris) at unscreened water diversions
Jamilynn B. Poletto, Dennis E. Cocherell, Timothy D. Mussen, Hossein Bandeh, M. Levent Kavvas, Joseph J. Cech, Jr., Nann A. Fangue
University of California, Davis, Department of Wildlife, Fish, and Conservation Biology, One Shields Avenue, Davis, CA 95616, (530) 752-3203, jbpoletto@ucdavis.edu
Replacing something that doesn't exist: regulatory, social, and biological issues for reintroduction of Chinook salmon into the San Joaquin River
Rhonda Reed
California Central Valley Office, 650 Capitol Mall, Suite 5-100, Sacramento, CA 95916. (916) 930-3609, Rhonda.Reed@noaa.gov
Water projects designed to extract freshwater for local urban, industrial, and agricultural use throughout the rivers and estuaries of California have contributed to the fragmentation and degradation of suitable habitat for native fish. The number of water diversions located throughout the Sacramento-San Joaquin watershed exceeds 3,300, and the majority of these remained unscreened. Many juvenile anadromous fish species are susceptible to entrainment into these diversions, impacting populations. Juvenile green sturgeon
Spring-run Chinook salmon (Oncorhynchus tshawytscha) were extirpated from the San Joaquin River over 60 years ago when Friant Dam operations were brought fully on line and large stretches of the river became dewatered. Remaining Central Valley spring-run Chinook salmon populations are listed as threatened under the Endangered Species Act (ESA). Fall-run Chinook salmon persist in dwindling numbers in the large tributaries to the system, but are not listed under the ESA. A legal settlement calls for the reintroduction of these salmon runs. The enabling statute requires use of the ESA experimental population designation and 4(d) rule to avoid impacts to third parties that could result from such reintroduction. The first use of an
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experimental population designation for an anadromous fish was completed in 2012, and the San Joaquin River spring-run final rule was published in 2013. Significant challenges exist to address these requirements while successfully establishing the new runs. Various methods were employed to obtain sensitive information needed for crafting these rules, while protecting proprietary information, and creative approaches are required. These methods may be useful to other efforts to develop safe harbor or experimental population rules for highly migratory and anadromous fish species. incorporating artificial barriers and supported by extensive recent field surveys. We also assess linear stream occupation versus HUC-based areal characterization of occupied habitat as a measure of range loss in the Central Valley. An accurate understanding of historical and current constraints on distribution will provide us with the foundation from which to assess potential future threats and opportunities to consider for our stewardship of Pacific Lamprey into the future.
Ocean conditions and growth rates of Scott Creek Steelhead

Nicolas Retford, Sean Hayes, Brian Wells, Nate Mantua
University of California, Santa Cruz; NOAA Fisheries, SWFSC, 110 Shaffer Road Santa Cruz, CA 95060, (831) 420-3917, nicolas.retford@noaa.gov
Exploring the historical, current and future distribution of Pacific Lamprey in California
Stewart B. Reid, Damon H. Goodman
Western Fishes, 2045 East Main, Ashland, OR 97520, (541) 890-1669, WesternFishes@opendoor.com
Pacific Lamprey, (Entosphenus tridentatus), were once widely distributed in anadromous freshwaters of California. Currently, their broader range has contracted northwards to where the southernmost occupied habitat appears to be Big Sur, just south of Monterrey Bay. Similarly, the upstream elevational limit of Pacific Lamprey in otherwise suitable streams has contracted downstream, with lampreys no longer reaching previously occupied upper reaches in eastern tributaries of the Central Valley. Historical records and vouchered specimens of lampreys are uncommon and scattered. Unvouchered records of sub-adults have little value due to frequent misidentifications of other lamprey species generically identified as Pacific Lamprey. Even absence data from the literature is frequently unreliable, due to focus on other taxa and use of survey techniques that do not effectively sample lampreys. We have attempted to tease out the historical distribution of Pacific Lamprey in California through a combination of approaches, including examination of museum collections, review of historical accounts, consideration of potential natural barriers (physical and environmental), as well as application of elevational and hydrologic criteria based on known historical and current localities. We also assess use of documented salmonid distributions as surrogates, but find that, while informative, they are limited in their utility due to differences in habitat use and passage capabilities. In resolving the current distribution of Pacific Lamprey we have applied the above criteria,
Managing populations of anadromous, threatened steelhead, (Oncorhynchus mykiss), is primarily based on drivers of survival in freshwater habitats, however there is increasing evidence that stressors in the marine phase are equally important. Climate change, and inter-annual ocean oscillations (ENSO, PDO, NPDO) affect sea surface temperature distributions, and optimal foraging grounds for steelhead with direct consequences for growth. We correlate years of varying distributions of sea surface with ocean growth. This study investigates ocean growth plasticity using scale analysis from coastal California steelhead and compares variations among years spent at sea and factors that influence steelhead survival. We have developed a time series of annual ocean growth for adult steelhead from Scott Creek, Santa Cruz Co. from 2002-2012, and compared ocean growth with sea surface temperatures, and precipitation from first year at sea. Using circuli spacing (mm/day) we developed a model to compare individuals with varying growth rates, and years spent at sea, and using PIT tag recovery data we validated our growth estimates and ocean years. We found that Scott Creek steelhead show significant differences in growth (circuli spacing) across years. There also was a significant interaction with fish that had higher growth rates returning to spawn that following season. This diversity and plasticity of behavior within populations, and their connections with ocean temperatures of O. mykiss is essential in understanding the connectivity of steelhead across ecosystems.
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Collaborative efforts to provide cool water for holding spring-run Chinook salmon (Oncorhynchus tshawytscha) in Butte Creek, Butte County, California
Catalina E. Reyes, Clint Garman, Edward Cheslak
Pacific Gas and Electric, Co. 3401 Crow Canyon Road, Rm, 150E, San Ramon, CA. 94568, 925-808-8811, cerh@pge.com
Butte Creek has the largest self-sustaining population of returning spring-run Chinook salmon (Oncorhynchus tshawytscha; SRCS) in California. Butte Creek is also the location of Pacific Gas and Electric Companys (PG&E) hydroelectric Federal Energy Regulatory Commission Project 803. Typically, SRCS hold in deep, cool water pools in Butte Creek as early as mid-February to midSeptember. Once they arrive in Butte Creek, the challenge becomes surviving the warm summer water temperatures to spawn successfully. PG&E and California Department Fish and Wildlife have worked collaboratively in collecting data on estimates of holding adults, pre-spawning mortalities, spawning escapement, and water temperature distributions. PG&E has used this information and collaborated with the agencies to better manage PG&Es facilities so that operations benefit holding SRCS. This presentation describes the challenges encountered in 2013 due to the below normal water year and high numbers of returning adult SRCS (N=16,789), and illustrates a collaborative effort that has successfully addressed salmon management issues in Butte Creek.
investigations are uncommon along California. Blasting to support dredging or construction occurs infrequently. Pile driving is the most common loud sound source in the California aquatic environment. As a result, there has been considerable attention to measuring, controlling and studying the effects of these sounds on fish. This presentation describes the methods used to measure and characterize underwater sounds from these sources, as well as efforts to reduce these sounds or at least their adverse effects to aquatic species. The fundamentals of underwater sound are briefly described. This includes a presentation of the common sound descriptors used to characterize anthropogenic sounds: peak pressure, sound pressure levels expressed as root-mean-square (RMS) levels and sound exposure level (SEL) used to describe the amount of received sound energy. The complexities of sound propagation through these mostly shallow water environments are described. There have been substantial efforts to reduce underwater sounds. The past and current control efforts will be described, as well as the complexities of implementation.
Electrofishing with spheres, rings and rods: electrical fields of three common electrodes
Jim Reynolds
School of Fisheries and Ocean Sciences, University of Alaska Fairbanks. 864 Pemberton Drives, Spring Creek, NV 89815, (775) 777-9104, jbreynolds@alaska.edu
Underwater anthropogenic sound that may harm fish: fundamentals, monitoring and control
James A. Reyff
Illingworth & Rodkin, Inc., 1 Willowbrook Circle, Suite 120, Petaluma, CA 94954, (707) 794-0400, jreyff@illingworthrodkin.com
Human induced or anthropogenic sounds are common in coastal water bodies. Some of these sounds can harm fish and other aquatic species by causing physical injury. These include high impulsive sounds such as marine pile driving, use of air guns in seismic surveys, and blasting. Pile driving occurs as part of infrastructure construction (e.g., bridge construction or rehabilitation). Seismic surveys that are conducted for geotechnical
Spheres, rings and rods are the shapes most commonly used for electrodes in electrofishing. The effects of size and shape of these electrodes on electrical fields have not been adequately studies under controlled conditions. In a concrete hatchery raceway, I compared electrical fields in terms of voltage gradient (V/cm) for 15-cm and 30-cm diameter rings and spheres and 48cm and 96-cm long rods. Rings and rods consisted of four stock diameters: 3, 6, 10 and 13 mm. Identical pairs (e.g., two 15-cm spheres) were suspended 300 cm (rings and rods) or 500 cm (spheres) apart and energized with 120-V AC. In-water voltage was measured between each of the 18 electrode pairs and converted to voltage gradients. Voltage gradients were compared at 1 cm (hazardous to fish) from electrodes and at distances to 1.0 and 0.1 V/cm (inner and outer edges of the effective electrical field). Gradients at 1 cm were lowest for the 30-cm sphere (4-5 V/cm) and increased with decreasing stock diameter. Distances to
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0.1 V/cm were longest for the 30-cm sphere and 96-cm rods (up to 83 cm), followed by 30-cm rings (55-64 cm), 48-cm rods (46-61cm), and 15-cm rings (40-47 cm). All electrodes produced 1.0 V/cm at about 10 cm. Small stock diameters (3 and 6 mm) produced very high voltage gradients near the electrode, a greater hazard for fishes. Contrary to conventional wisdom, field size was more affected by electrode size and shape than stock diameter. Rings, compared to rods of equal stock diameter, produced smaller fields. Electrofishing-based projects aimed at small and juvenile fishes in shallow water will be more effective with smaller rings and rods made of smaller stock. Those aimed at larger fishes in deeper water should use larger rings or rods with larger stock diameter, or spheres. values to assign rearing locations of fish with unknown origins in the Shasta River. Juvenile Chinook salmon that reared in the upper basin had otolith 87Sr/86Sr values of 0.703-0.704, whereas juveniles that reared in the lower basin had 87Sr/86Sr values of 0.706-0.707. Juvenile Chinook salmon that reared in the lower or upper Shasta River basin are identifiable by the distinct differences in 87Sr/86Sr values incorporated into the juvenile region of the otoliths. This project demonstrated the potential to use otolith isotope analysis to identify how life history differences between juvenile Chinook salmon that rear in the upper or lower Shasta River basin may affect marine survival and adult returns.
Rearing location of juvenile Chinook salmon within the Shasta River basin as determined by otolith strontium isotopic ratio analysis
C. Meiling Roddam, Darren M. Ward
Humboldt State University, Department of Fisheries Biology, 1 Harpst St, Arcata, CA 95521, (310) 210-1652, mr61@humboldt.edu
Collaborating in rough seas: can the Yuba Salmon Forum succeed in restoring Yuba salmon?
Steve Rothert
American Rivers, 120 Union Street, Nevada City, CA 95959, (530) 277-0448, srothert@americanrivers.org
The Shasta River is one of the most productive tributaries of the Klamath River for Chinook salmon (Oncorhynchus tshawytscha). There are two primary spawning and juvenile rearing areas for Chinook salmon in the Shasta River: the lower basin canyon area and the upper basin Shasta-Big Springs complex. The distinct geology of the upper and lower Shasta River basin provided a unique opportunity to distinguish fish originating from these rearing locations due to the distinct strontium isotope ratio (87Sr/86Sr). 87Sr/86Sr in stream water collected in March 2012 and 2013 was 0.704 (precision of 0.000031) and 0.706 (precision of 0.000019) for the upper basin and the lower basin respectively. Juvenile Chinook salmon otoliths that were collected from outmigrating fish at the mouth of the Shasta River had unknown rearing locations (they could have been from either the upper or lower basin), whereas otoliths collected from fish in the upper basin were presumed to have reared in the upper basin. Otolith 87Sr/86Sr values were measured by laser ablation MC-ICPMS technique. Measurements of 87Sr/86Sr values subsequent to the exogenous feeding check from each otolith were averaged, and compared to the stream water 87Sr/86Sr
The Yuba River once supported hundreds of thousands spring-run and fall-run salmon, steelhead trout and other native fish. Since the hydraulic mining era in the mid-1800s, this watershed has been altered dramatically and now supports over 15 dams that provide water, power and flood protection. Salmonid populations have declined significantly, and are now limited to the lower Yuba River below the Corps of Engineers Englebright Dam. Spring-run salmon and steelhead trout are listed as threatened under the Endangered Species Act. River advocates, water and power companies and fishery agencies have disputed whether and how to restore salmon and steelhead to the upper Yuba watershed. The dispute has spawned multiple lawsuits and affected several hydropower-relicensing proceedings. In 2010, however, Yuba watershed stakeholders decided to explore a new approach to identify potential pathways. With support from the National Marine Fisheries Service, the Yuba Salmon Forum was born. The Yuba Salmon Forum has led to unprecedented progress in California toward the potential reintroduction of salmon and/or steelhead into the
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upper watershed. The Yuba stakeholders, who at times are battling in court or in regulatory proceedings, committed to a collaborative process to identify, evaluate and seek to achieve salmonid restoration strategies throughout the watershed. We have completed an assessment of potential salmonid habitat and fish passage alternatives, and now the question for the Yuba Salmon Forum is: can we work together to take action to restore Yuba salmon?
Non-natal estuary preferences of SDPS and NDPS green sturgeon

Andrea Schreier, Olaf Langness, Bernie May
Genomic Variation Lab, University of California Davis One Shields Ave, Davis, CA 95616. (530) 752-0664 amdrauch@ucdavis.edu
Interactive effects of a non-native predator and habitat alterations on native juvenile salmon
Megan Sabal, Sean Hayes, Joseph E. Merz, JD Setka
UC Santa Cruz, 212 Anita St., Santa Cruz, CA 95060, (847) 6481748, megan.sabal@noaa.gov
Predation is a fundamental process that structures and shapes ecosystems. Humans can intensify effects of predation on native species through introduction of non-native species and habitat alterations. In California, native salmon populations are in decline and juvenile salmon experience low survival during their outmigration where they pass through various habitat alterations and encounter non-native predators (e.g. striped bass). My study objectives were to (1) examine how striped bass consumption of juvenile salmon varies by habitat; and (2) assess population-level consumption in an area of high predation. Diet data illustrated a significant difference in frequency of occurrence of important prey items for striped bass caught at a dam (Chinook salmon 80%, crayfish 15%) and other locations (Chinook salmon 0%, crayfish 75%). Focusing on the dam habitat, population-level consumption of striped bass on juvenile salmon was examined through three separate approaches resulting in a range of impacts between 10% and 29%. These results show that humans are exacerbating mortality on native juvenile salmon through combined effects of a non-native predator and habitat alterations. Predators, prey, and habitat can interact to shift predation pressure; this has important implications in assessing relative potential for various management strategies for native species recovery.
Green sturgeon are known to congregate in estuaries along the West Coast, many of which do not themselves possess spawning populations. Telemetry studies of others have shown differences in non-natal estuary use between SDPS and NDPS adult green sturgeon. Here, we use genetic data to determine DPS origin of 180 juvenile and adult green sturgeon captured in the Lower Columbia, Willapa Bay, and Grays Harbor from 20102012. Overall, the majority of green sturgeon we examined were assigned to the SDPS (62%). There was no significant difference in DPS composition between Lower Columbia and Willapa Bay, where the majority of green sturgeon sampled originated from the SDPS. Grays Harbor contained more NDPS than SDPS green sturgeon, which differed significantly from the composition observed in the Lower Columbia and Willapa Bay. When all individuals were sorted by fork length frequency, the majority of green sturgeon <1 m originated from the NDPS. Future analyses will examine the relationship between DPS designation and sampling date to evaluate potential seasonal shifts in estuary use between populations.
Predation and gut evacuation rates as measured by acoustic tags in the Tracy Fish Collection Facility Primary Channel
Andrew Schultz, Kevin Kumagai
U.S. Bureau of Reclamation, Tracy Fish Collection Facility, Byron, CA. 16650 Kelso Rd. Byron, CA 94514, (209) 836-6224, aschultz@usbr.gov
In the Sacramento-San Joaquin Delta, several salmonid species are listed as threatened or endangered. One potential cause of lower juvenile salmonid survival may be striped bass predation. Acoustic tags are routinely used to estimate survival by releasing and detecting tagged juvenile salmonids with the assumption that tagged salmonids are not consumed by other fishes. If this assumption is violated, salmonid survival estimates may be misinterpreted. A key consideration is the time taken by an acoustic tag to pass through the digestive
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tract of a predatory fish. To measure evacuation rates, acoustically tagged juvenile Chinook salmon were euthanized, then tethered and fed to free swimming (acoustically tagged and wild) striped bass in the primary channel of the Tracy Fish Collection Facility. Confirmation of time at predation event was determined by analysis of 2D acoustics tracks. The amount of time required for an acoustic tag to pass through the digestive tract of a striped bass estimated the evacuation rate. Mean tag evacuation time was 1.8 d (n = 14; SD = 0.49; range = 1.2 to 2.7). Mean tagged salmon was 146.6 mm FL (n = 14; SD = 7.6; range = 131 to 165). Results indicated free swimming striped bass evacuate small acoustic tags (0.5 g) relatively quickly in 22C water. By comparison, a study investigating predation events using larger tags (1.1 g) on relatively sedentary laboratory fish held in 16C had greater evacuation times. This feasibility study demonstrated acoustic tags can provide information about predation and gut evacuation in free-swimming predatory fish. As a result, the Bureau of Reclamation extended testing of predation and gut evacuation rates to include temperature variation and food availability levels in the Tracy Fish Collection Facility Primary Channel, starting late 2013. from here? The solution to this question is tied to how common perception, political, monetary, and regulatory factors will combine with this newer data about Feather River green sturgeon. The response has the potential to affect both species and river management which can have an overall impact on green sturgeon conservation and the status of the species.
Evolution on the Mokelumne River: from litigation to collaboration

Jose Setka
East Bay Municipal Utility District, 1 Winemasters Way, Suite K, Lodi, CA 95240, jsetka@ebmud.com
Are green sturgeon found in the Feather River only during wet water years? Myth busters and its implications
Alicia Seesholtz
Department of Water Resources; 3500 Industrial Blvd, West Sacramento, CA 95691; (916) 3769848, alicia.seesholtz@water.ca.gov
Management of the southern Distinct Population Segment of green sturgeon in the Feather River has become a focus of recovery for this species. Most documents written about green sturgeon suggest that the species uses the Feather River only in wet water years. However, information gathered in the past decade has shown that sturgeon can be found in the system during all water year types. The number of fish using the river in a typical year appears to be very low (<10). Results of data collected over the past several years using telemetry, artificial substrates, and DIDSON surveys are providing insight into spatial and temporal distribution and habitat utilization. Our project is helping to dismantle many misconceptions about green sturgeon behavior in the Feather River and is presenting us with our next challenge: How do we move forward
Since the 1980s, the management of the Lower Mokelumne River has evolved from an adversarial and litigious process, to a result driven highly successful collaborative partnership. The Lower Mokelumne River Partnership (LMRP) members (EBMUD, CDFW, USFWS, NMFS) and numerous stakeholders have implemented a number of significant rehabilitation and research programs within the watershed. In order to accomplish these projects and programs, each entity has had to commit to making key changes to its approach and, in some cases, fundamental changes to the organizational culture regarding resource management. The results have not only been deemed successful in various forums, but have allowed the LRMP and its stakeholders to geographically expand their work into the Sacramento San Joaquin Delta and Upper Mokelumne River. Along the way the stakeholder and collaborative partnership has grown to include local irrigation districts, land owners, and Non-Governmental Organizations. This discussion will focus on the conditions leading up to the formation of the LMRP, provide examples of successes based on collaborative approaches, and layout a framework for addressing future challenges in the Mokelumne River watershed.
The power of SNPs to understand past stocking and contemporary status of native trout populations
Molly Stephens, Bernie May
Genomic Variation Laboratory, University of California, Davis, Dept. of Animal Science, One Shields Ave. Davis, CA 95616, (530) 754-4155, mrstephens@ucdavis.edu
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Much has been learned over more than three decades of genetic research on Californias native trout species. Population structure, genetic diversity, and introduced hatchery rainbow trout influence have been illuminated using allozyme, microsatellite and small-scale SNP studies. Genetic studies are now transitioning to the use of large scale single nucleotide polymorphisms (SNPs) to improve our ability to reconstruct genetic relationships among taxa and populations, infer important demographic parameters, and improve our ability to conduct genetic monitoring of trout populations into the future. Genetic monitoring of threatened golden and redband trout populations will be discussed, with an emphasis on how SNP data may be used for management decisions in these species. sightings still occur annually with adult green sturgeon consistently observed in the estuary and over one hundred kilometers upstream, consistent with a spawning run. This project will address one of the primary green sturgeon data gaps by investigating the best potential undocumented spawning run. For whatever green sturgeon that do still spawn in the Eel River, it is important to determine if they are northern DPS, as presumed without direct evidence, if they are southern DPS, or even a mix. All possible outcomes would be significant: 1) if they are northern DPS then this would add a third spawning river to that population besides the Klamath and Rouge rivers; 2) if they are southern DPS then that would add a vital second spawning population besides the Sacramento River, with important implications for resiliency; and, 3) if they are a mix, then it would be the first documented mixed spawning run. In addition to determining the population of origin and numbers of spawners, its important to document spawn timing and locations, which can allow for a more accurate assessment of potential threats to successful reproduction and recovery of green sturgeon in the Eel River and subsequent restoration actions.
Planning for Implementation

Phil Stevens
Urban Streams Council, 820 Delaware St., Berkeley, CA 94710, (510) 356-0591 x2, phil@urbancreeks.org
Too often, restoration plans result in big binders on a shelf but no implemented projects. Major barriers to implementation include lack of adequate funding, permitting challenges, weak community support, and concerns about long-term maintenance. This session will explore how one agency-NGO partnership is addressing these challenges to restore and enhance aquatic and riparian habitat on a landscape scale.
Real-time 2-dimensional tracking in the tailrace of a hydroelectric dam

Kevin Kumagai, Colleen Sullivan
HTI, 715 NE Northlake Way, Seattle, WA 98105, (206) 633-3383, kkumagai@HTISONAR.COM
Status and Origin of Green Sturgeon of Eel River Basin: Myth or Mystery?
Joshua Strange, Stephen Kullman, Ethan Mora
850 G Street, Suite K, Arcata, CA 95521, (707) 269-6109, jss@stillwatersci.com
The goal of this 3-year project is to determine the current status and population of origin of North American green sturgeon (Acipenser medirostris) in the Eel River of northern California. Green sturgeon in the Eel River comprise one of the most prominent data gaps for North American green sturgeon given that the Eel River is one of the larger rivers in California and had an apparently robust historic spawning run. Ambiguity continues in terms of the current status of green sturgeon in the Eel River, with official designations considering the spawning run lost and of northern Distinct Population Segment (DPS) origin, and yet
A hydropower tailrace is a challenging sampling environment for any scientific methodology. Using acoustic telemetry to track individual fish with submeter resolution and in 2-dimensions (2D) within this environment would appear infeasible. Notable challenges include significant levels of entrained air and turbulence, shallow water, large angular stream-bed substrate, and possible non-reverberant noise from power production. These noise impacts can be minimized by using acoustic tags that are fullyprogrammable and utilize the pulse-repetition period method. Overcoming these obstacles successfully was highlighted in a recent single-day assessment, where we deployed, tested and real-time 2D tracked acoustic tags in the tailrace of a hydroelectric dam. Animated 2D tracks produced in real-time will be presented and compared with overlaid post-processed tracks.
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These results demonstrate that acoustic tags using the pulse-repetition period method is an efficient and excellent tool to 2D track in a complex and noisy tailrace environment. of larger adult returns following wetter outmigration years.
Life history portfolios within salmon populations: when do different outmigration phenotypes contribute?
Anna M. Sturrock, JD Wikert, T. Heyne, C. Mesick, PK Weber, G. Whitman, RC Johnson
Institute of Marine Sciences, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, (510) 423-2210, sturrock@ucsc.edu
Back from the brink challenges, collaborations and solutions for salmon recovery in California
Stephen Swales
Fisheries Branch, California Department of Fish & Wildlife, 830 S Street, Sacramento 95811, (916) 324-6903, Stephen.swales@wildlife.ca.gov
The maintenance of life history diversity within and among populations is thought to be critical for the longterm persistence of salmon stocks. Asynchronous population dynamics can buffer stocks against environmental change and provide a stabilizing portfolio effect. Preserving and restoring diversity in life history traits is thus central to many recovery efforts, but it is necessary to first understand the way in which environmental factors affect their expression and success. Juvenile Chinook salmon leave their natal rivers at different sizes, ages and times of the year. Rotaryscrew trap (RST) sampling in the California Central Valley has indicated that in wetter years, most juveniles emigrate as fry (<55mm), while in drier years a greater proportion emigrate as parr (>55-75mm) and smolts (>75mm). Here, we used otolith (earstone) Sr isotopes in adult Chinook salmon returning to the Stanislaus River to determine the influence of river conditions on juvenile outmigration patterns, habitat use and survivorship. Paired otolith and scale samples were used to reconstruct size-resolved juvenile migration patterns of successful salmon in a wetter (2000) and drier (2003) year. For each returning adult, the size at which it had left its natal tributary was reconstructed by coupling otolith Sr isotope and radius measurements. The proportions of fry, parr, and smolt captured at RSTs were compared with those reconstructed in the adults from the same cohort, and used to estimate survivorship. Juvenile abundance, size and phenology varied largely as a function of hydroclimatic regime, while survivorship appeared driven by environmental factors as well as size- and time-selective mortality. While fry survival is generally assumed to be negligible in this system, our data indicate that they can represent more than 20% of the adult returns in a wet year. This result might partly explain the long-recognized pattern
Pacific salmon and steelhead are in serious decline throughout California, with many populations already extirpated and many others heading towards extirpation in the near future. The likely causes of these declines are well established, and center around the adverse effects of human disturbances to land and water resources, which have resulted in severe losses and degradation of suitable habitat conditions for both juveniles and adults, at nearly all stages of the life-cycle. In the last several decades, habitat restoration and rehabilitation programs have been widespread in many California watersheds, in attempts to restore suitable habitat conditions. Yet, despite the expenditure of many millions of dollars in habitat restoration programs, salmon populations continue to decline. Why? What can be done to prevent the loss of our salmon stocks? This paper examines the many challenges to salmon recovery in California, and discusses the importance of inter-agency collaboration, with particular focus on the recovery of salmon populations in coastal watersheds of central and northern California. California Department of Fish and Wildlife, NOAA Fisheries and a wide variety of stakeholders are currently collaborating in PACT Priority Action Coho Team a recovery program which is attempting to prevent further extirpation of coho salmon populations in the Central California Coast ESU, where coho salmon are endangered. Increased interagency collaboration such as this is essential if salmon recovery in California is to succeed.
Movement behavior of juvenile green sturgeon in the Central Delta

Michael J. Thomas, Matthew L. Peterson, A. Peter Klimley
University of California, Davis, Biotelemetry Laboratory, 1088 Academic Surge, Davis, CA, (530) 752-5372, mjthomas@ucdavis.edu
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Since the ESA listing of green sturgeon in 2006, many new studies have been developed to formulate a better understanding of the biological and ecological needs of green sturgeon within their broad range. It is not serendipitous that many of these new studies have focused the development of new information on the adult life stage. Despite their cryptic behavior, extreme habitat ranges, and relatively low numbers, adults are more readily available and hence easier to study. Alternatively the juvenile life stage has been largely ignored outside of laboratory studies. In many respects this is attributed to the general lack of individuals with which to study and a very poor understanding of both when and where juveniles could be targeted throughout the putative nursery grounds of the Delta and Bay. We present here our findings for the first telemetry study conducted on juvenile green sturgeon in the California Delta. Through the use of continuous shipboard tracking we describe the movement behaviors of 6 wild green sturgeon near the Santa Clara Shoal complex, an area within the Central Delta where there are historical records for the presence of juvenile green sturgeon. Additionally we employ both parametric and nonparametric mixed models to explain the differences in movement patterns and habitat use. information then contributes to development of fishing regulations to achieve co-equal objectives of utilization and conservation of this resource. This study focuses on Sacramento River fall-run Chinook salmon and addresses questions about how fishing effort, catch, and harvest respond to variable long-term abundance of Chinook salmon. Our analyses provide evidence of highly deterministic non-linear relationships between fall-run Chinook salmon abundance and both fishing effort and catch of salmon. Simple models indicate that when abundance is very low, both fishing effort and catch are low. Effort and catch increase with abundance until, in both cases, the relationship approaches an asymptote at high escapement levels, suggesting that there is a limit in the collective ability of river sport anglers to fully exploit the resource when abundance is very high. Anglers also become increasingly picky with regard to Chinook salmon that they harvest. This relationship is reflected in a very strong linear fit between the number of salmon released in the sport fishery and the number caught. When considered in relation to Chinook salmon fishing regulations, we conclude that this fishery is indeed largely self-regulating as a function of Chinook salmon abundance.
Is the Sacramento River fall-run Chinook salmon sport fishery self-regulating?

Rob Titus, Mike Brown, Jason Azat
California Department of Fish and Wildlife Fisheries Branch, 8175 Alpine Avenue, Suite F Sacramento, CA 95826, (916) 227-6390, Rob.Titus@wildlife.ca.gov
Alternative use of sonar in detection and discernment of fish species in short range, turbid areas, with the Adaptive Resolution Imaging Sonar ARIS short range units
Gretchen Umlauf
National Marine Fisheries Service, 650 Capitol Mall, Suite. 8300, Sacramento, CA 95814, (916) 930-5646, Gretchen.Umlauf@noaa.gov
The Sacramento River system in Californias Central Valley is the States greatest producer of Chinook salmon (Oncorhynchus tshawytscha) and supports one of the largest river fisheries for this native species on the West Coast. Within its salmon management program, California Department of Fish and Wildlife estimates the annual escapement of spawning Chinook salmon to Central Valley rivers, and fishing effort, catch, and harvest of Chinook salmon in the Sacramento River sport fishery. Understanding the relationship between Chinook salmon abundance, as indexed through escapement monitoring, and basic parameters of the river sport fishery provides the basis for making predictions about how the sport fishery will respond with variable Chinook salmon abundance. This
The higher resolution and lower power requirements of the ARIS short range units are ideal for studying fish movements in the turbid waters around tidal flap structures and fish passes, particularly in remote locations that lack mains power supply. All the new ARIS Explorer range of sonar's are low powered, drawing less than 15W half the nominal 30W required for the current DIDSON. It also requires less maintenance as the sealed lens arrangement eliminates the need for a silt box and the internal focus drive mechanism avoids potential issues. The ARIS features, applications and costs will be reviewed in this session. Examples of splits and video feeds will also be shown in this session.
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Successes and challenges of fisheries resources in a large restoration project
Laura Valoppi, Jim Hobbs, John Bourgeois, Eric Mruz
U.S. Geological Survey, Western Ecological Research Center, 6000 J Street, Placer Hall, Suite 4001, Sacramento, CA 95819, (916) 278-3124, Laura_Valoppi@usgs.gov
Use of DIDSONTM to evaluate fish screens, water diversions, juvenile salmon rearing, and predatory fish
Dave Vogel
Natural Resource Scientists, Inc., P.O. Box 1210, Red Bluff, CA 96080, (530) 527-9587 x12, dvogel@resourcescientists.com
The South Bay Salt Pond Restoration Project has several local, state, federal and non-profit collaborators that are faced with multiple challenges for the management of fisheries resources while seeking to restore 15,000 acres to a mix of managed ponds and tidal marsh. This presentation will describe the challenges the collaborators face and the solutions we have put in place so far. Monitoring of fisheries resources over the last 3 years has found that management actions have transformed these ponds into an important and productive area for San Francisco Bay fish species. Restoration has provided > 1,800 acres of habitat for 58 species, with > 85% native species, including the State-listed longfin smelt. Restored ponds are quickly used by fish to feed and recruit young fish, productivity inside the ponds is attracting fish which is transferring up the food chain and providing benefits to fish in the bay. In particular, the Alviso Complex is a highly productive area. However, the Project also faces challenges of managing the ponds to avoid impacts on steelhead smolt that are out-migrating from the Guadalupe River into Alviso Slough. We have begun a steelhead smolt study using PIT-tagged smolt and RFID antennas around the water control structures of a 1400 acre pond to track movement of out-migrating steelhead smolt. In another set of ponds in the Alviso Complex, fall-run Chinook salmon have been entering a pond at low-tide through the outflow water control structure consisting of a weir box with a flap gate. Some of these salmon have been rescued, some have perished inside the pond, some have traversed the pond to the inlet structure and have been blocked from exiting by a fish screen intended to keep migrating fish from entering the pond through the inlet.
The use of DIDSONTM for fishery research in the Sacramento River and Sacramento San Joaquin Delta has provided valuable insights into problems affecting anadromous salmonids. Factors adversely impacting the survival of salmonids have been difficult to evaluate due to the inability to visually examine habitats where young salmon reside because of reduced water clarity, swift water, insufficient field of view, or disturbing normal fish behavior using traditional methods (e.g., SCUBA/snorkel, underwater videography). DIDSONTM footage has been used to evaluate large-scale Sacramento River fish screens and helped to pinpoint localities where predatory fish can prey on young salmon. The resultant findings will lead to structural improvements for increased fish survival. For water diversions that remain unscreened, DIDSONTM footage has helped to discern intake features that will assist in prioritizing the most-important diversions where fish screens should be installed. The interaction between predatory fish and rearing juvenile salmonids has been documented with use of DIDSONTM that previously was not possible. The customized design of a pan-and-tilt mechanism to operate a DIDSONTM camera in swift water from a jet boat greatly expanded the opportunities to obtain sonar footage of fish in their natural and altered habitats. It is highly recommended to practice taking sonar camera footage on inanimate submerged objects to interpret acoustic reflections and shadows. To obtain the greatest benefit from DIDSONTM, it is helpful to use the technology in combination with other fishery resource evaluation tools to improve species identification and assess behavior. Examples of sonar camera footage are provided to demonstrate how DIDSONTM has improved our understanding of factors affecting juvenile salmon habitats and the formulation of measures for remedial actions to increase fish survival in locales often inaccessible to researchers.
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Riverscape genetics identifies two genetically divergent groups and a contact zone in Klamath River speckled dace (Rhinichthys osculus)
Jesse Wiesenfeld, Andrew Kinziger
Humboldt State University, 1 Harps St Arcata, CA, 95521, (503) 502-8128, jcw352@humboldt.edu
Challenges, collaboration, and solutions in the FERC relicensing process

Scott D. Wilcox
Stillwater Sciences, 279 Cousteau Place, Suite 400, Davis, CA 95618, 530-756-7550, scott@stillwatersci.com
The turbulent geologic and climatic history of the North American west has greatly impacted the biogeography of freshwater fishes. We examined riverscape levels of genetic structure of speckled dace (Rhinichthys osculus) in the Klamath River basin, including the Trinity River, the largest tributary of the Klamath River. Previous studies have suggested the existence of distinct genetic groups of speckled dace in the Klamath River basin but the number of locations sampled was insufficient to resolve the distribution and potential contact zones between the groups. We assayed variation in the mitochondrial cytochrome b gene (618 bp) and in 8 microsatellite loci among 24 speckled dace populations. Analysis supported the presence two divergent groups in the Klamath River basin, one restricted to the Trinity River and the other occurring in the Klamath River proper and its tributaries. Patterns of divergence were congruent in both nuclear and mitochondrial markers and the extent of mitochondrial divergence was consistent with levels observed between described species (2 %). Genetic analysis did detect a contact zone near the confluence of the Trinity and Klamath Rivers, but hybrids appear to be rare (or nonexistent). A reproductive isolating mechanism responsible for maintaining these distinct genetic groups is unknown and needs to be examined further. The Trinity River speckled dace exhibited substantially lower heterozygosity (He =0.53 ) and allelic richness (Ar =8.67 ) than the Klamath speckled dace (He = 0.71; Ar =11.71 ). Given these divergence in the two groups, it is possible that the Trinity River speckled dace represent a different colonization event separate from the Klamath River speckled dace, before the rivers were in contact. This interesting genetic relationship between these two lineages of speckled dace presents a unique chance to study the evolutionary consequences of the Klamath basins geologic past.
FERC relicensing provides a perfect case study of challenges, collaboration, and solutions involved in resource management, with fisheries management frequently taking center stage in the process. This session will provide examples of tools used to address some of these challenges, including tools for dealing with conflicting water demands, data overload, and sampling limitations. Collaboration is a large part of the FERC process, and can either improve the process or bog things down; examples and perspectives on how to best collaborate will be explored. Finally, relicensing offers the opportunity to solve fisheries management and other resource problems on a larger scale, but those solutions can be elusive for a variety of reasons. Examples of what has worked to solve problems and where we need to improve our processes and scientific methods will be presented and discussed.
Potential effects of future climate change on salmonids in Californias Central Valley

Rick Wilder, Cathy Marcinkevage
ICF International, 630 K Street, Suite 400, Sacramento, CA 95814, (916) 231-9612, rick.wilder@icfi.com
Potential effects of future global climate change are a major concern for cold-water anadromous fish species with restricted access to cooler historical spawning and rearing habitat. By employing a novel technique for evaluating exceedances of regulatory temperature thresholds, we assessed potential temperature-related effects of future climate change on multiple threatened and endangered salmonids in the upper Sacramento, Feather, and American rivers. Our analysis predicts that salmonids will experience a consistent two- to threefold increase in suboptimal temperature conditions during much of their upstream freshwater residence over the next 50 years. We offer potential solutions for improving the likelihood of sustaining Central Valley salmonid fisheries in the future. We found that our analytical technique could be an effective screening tool
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for biological evaluation because of similarities in results to more elaborate biological models, but without the additional effort needed to run those models.
Is recovery of green sturgeon possible?

David Woodbury
NOAAs National Marine Fisheries Service, West Coast Region, California Coastal Area Office, 777 Sonoma Avenue room 325, Santa Rosa, CA 95404, (707) 575-6088, David.P.Woodbury@noaa.gov
A federal recovery plan is being developed for the threatened southern Distinct Population Segment of North American green sturgeon. When approved, the plan will describe the threats the species faces and identify prioritized actions that might be taken to recover the species. The greatest threats to the species occur within the Sacramento River watershed, where two of the largest dams in the nation block access to historical spawning sites and current water management practices result in hydrographs and thermographs that bear little resemblance to those prior to dam construction. A discussion regarding these threats will be provided. Given the complexity of water management within the Central Valley, the likelihood of recovering green sturgeon is a reasonable question to consider.
important factors that influence the potential for noise to injure fish. The frequency range and source noise level of 160 dB re 1Pa SPLrms at 1 meter of tidal turbine noise would generate sound detectable by fish. Noise sublethal and lethal affects in fish manifest in many ways, such as threshold shift in auditory sensitivity or tissue damage. The goal of this study was to determine if noise generated by a 6 m diameter OpenHydro turbine cause injuries to juvenile largemouth bass tissues or Chinook salmon tissue and hearing. After 24 hrs of exposure to simulated tidal turbine noise, the both species were examined for tissue injury, or the hearing was measured of juvenile Chinook salmon. The simulated noise exposure did not traumatize tissues in either juvenile species, or the hearing of Chinook salmon. These results help to develop environment regulations for assessing potential impacts and effective mitigation.
Successes from a low head dam removal project on an ephemeral Mokelumne River tributary in the Central Valley of California
Michelle L. Workman, Robyn Bilski, Joseph E. Merz
East Bay Municipal Utility District. 1 Winemasters Way Suite K. Lodi Ca. 95240. (209)365-1467, mworkman@ebmud.com
Effects of short-term tidal turbine noise on fish tissues and hearing

MB Halvorsen, TJ Carlson, Christa M. Woodley
Pacific Northwest National Laboratory, Marine Sciences Laboratory, Sequim, WA USA, (360) 681-3603, christa.woodley@pnnl.gov
Noise in the aquatic environment is a known stressor to many types of aquatic life, including marine mammals, fish, and birds. Prototype tidal turbine deployments into high tidal flow locations are planned in Puget Sound, U.S.A. There are a number of transient and resident ESA protected marine mammals and fish at the proposed sites and in the immediate surrounding area. Two of these species, juvenile Chinook salmon (Oncorhynchus tshawytscha) and largemouth bass (Micropterus salmoides) were chosen to study the physiological effects of exposure to tidal turbine noise. The characteristics of noise, i.e., spectra and level, are
Large dam removal projects involving the reconnection of habitat in salmon-bearing watersheds have received much interest in recent years as a means to sustain populations. For this presentation, we discuss the removal of a low head dam to reopen a small ephemeral tributary to the Mokelumne River California that historically supported small numbers of adult Chinook salmon (Oncorhynchus tschawytscha) and steelhead (O. mykiss). Project elements included: removal of a low head dam and other smaller passage obstructions within three miles of the confluence with the lower Mokelumne River, increasing native vegetation canopy cover to encourage cold-water fisheries, increasing native shrubs to improve habitat for neotropical migratory birds, physical removal of nonnative plant species, limiting livestock access to riparian zones and repairing minor erosion/bank instability to reduce creek sedimentation. Percent of habitat available, shifts in fish community, and documented use by adult and juvenile salmonids will be discussed.
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Fisheries investigations conducted in the San Joaquin River Restoration Area and their relation to salmon reintroduction in the San Joaquin River
Michelle Workman, Zachary Jackson
East Bay Municipal Utility District. 1 Winemasters Way Suite K. Lodi Ca. 95240. (209)365-1467, mworkman@ebmud.com
One of the goals of the San Joaquin River Restoration Program (SJRRP) is to restore and maintain fish populations in good condition in the mainstem San Joaquin River below Friant Dam to the confluence with the Merced River, including naturally reproducing and self-sustaining populations of salmon and other fish. To facilitate reintroducing both spring run and fall run Chinook salmon to the San Joaquin River, a number of fisheries studies are currently ongoing to provide information to inform these reintroduction and potential restoration actions. This presentation will highlight the results of ongoing studies related to predator populations as well as studies of juvenile and adult salmonid habitat use in the past few years.
the spring snowmelt recession in eight unregulated rivers across the range of the Sierra Nevada and found unregulated systems behaved similarly with respect to seasonal patterns and flow recession shape (i.e., recession limb curvature). Thus, spring recession flows can be modeled in regulated systems using a daily percent decrease in flow metric that mimics those predictable characteristics. We tested the methodology by creating a series of flow recession scenarios and evaluating the distribution and diversity of hydraulic habitat through time within a two-dimensional hydrodynamic model at a regulated river study site. The results show that flow recessions with slow ramping rates (less than 10% per day) were most protective of crucial Foothill yellow-legged frog breeding habitat and provided the most diverse hydraulic habitat spatially and temporally, which is vital to support native species guilds and maximize aquatic biodiversity. The methodology described in this study has recently been utilized within the FERC process to create flow recessions that more naturally transition from high spill flows to minimum instream flows.
Management of the Spring Snowmelt Recession in Regulated Systems

Sarah M. Yarnell, Ryan A. Peek, Amy Lind
Center for Watershed Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, (530) 754-9367, smyarnell@ucdavis.edu
In unregulated rivers in the Sierra Nevada mountains of California, the spring snowmelt recession links high winter flows to low summer baseflows and is a consistent and predictable portion of the annual hydrograph. Consequently, it is an important resource to both riverine ecosystems and Californias water supply. In regulated river systems where the spring snowmelt recession is often captured behind dams or diverted for hydropower, restoration of a more natural spring flow regime can provide distinct ecological benefits, such as breeding and migration cues, increased habitat availability, and greater hydraulic habitat diversity. However, knowledge of how to create and manage an ecologically beneficial spring snowmelt recession in regulated river systems has been lacking. Using fundamental flow components such as magnitude, timing and rate of change, we quantified
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Poster Presentation Abstracts

Comparing juvenile green and white sturgeon performance at a simulated angled louver; behavioral deterrents and water velocity effects
Tommy V. Agosta, Dennis E. Cocherell, Nann A. Fangue, Jamilynn B. Poletto, Joseph J. Cech Jr.
Wildlife, Fish, and Conservation Biology Department, 1088 Academic Surge, University of California, Davis, One Shields Avenue, Davis, CA 95616, (925) 963-1621, tvagosta@ucdavis.edu
We are investigating the swimming performance of sturgeon species to help resource managers develop criteria for promoting their conservation
Sarah E. Baird, Jamilynn B. Poletto, Christine E. Verhille, Dennis Cocherell, Joseph Cech Jr., Nann A. Fangue
University of California, Davis, 1088 Academic Surge Depart of Wildlife, Fish, and Conservation Biology One Shields Ave, Davis, CA 95616, sebaird@ucdavis.edu
In Californias Central Valley Watershed the myriad of water diversions have the potential to entrain (i.e. pull through) migrating juvenile white and green sturgeon (Acipenser transmontanus and Acipenser medirostris, respectively). Louvers are increasingly being considered as a methodology to guide fish away from diversion intakes, reducing or preventing entrainment. We conducted experiments to examine sturgeon entrainment rates, louver interactions, and if a behavioral deterrent could modify sturgeon responses. Experiments, n=35 for each treatment, were in a smallscale flume containing a louver model (2m long) and operated at three water velocities (20cm/s, 40cm/s, and 60cm/s). Our behavioral deterrent was a strobe light set to 300 flashes per minute. Strobe lights are widely used as a sensory deterrent for guiding fish away from target areas, though research on their effectiveness is mixed. Our results showed that juvenile white sturgeon contact louvers twice as often as green sturgeon (mean 14-16 cm TL). However, white sturgeon were less likely to become impinged or be pulled through the louver compared to green sturgeon. When compared to control experiments, strobe lights had a minimal effect as a behavioral deterrent. Green sturgeon were only 11% more likely to bypass louvers with strobe lights, compared to 9% for white sturgeon. Experiments analyzing the mechanisms of fish interactions at diversions are of particular importance to sturgeon stocks in California. Our experiments suggest that interactions with and entrainment through louvers may be a concern for wild sturgeon. In particular, green sturgeon population numbers are low and these fish are occasionally entrained at Delta water export facilities. These data also lay the foundation for laboratory experiments using full-scale louvers to better provide water intake operators and fisheries managers with information on the effectiveness of angled louvers, as well as whether or not strobe lights are suitable behavioral deterrents for sturgeon near water intakes.
North America sturgeon populations have been declining over the last several decades. Recruitment failure, especially at early life stages, has been identified as a major contributor to these declines. Because locomotion plays a key role in the ability of fishes to forage, escape predators, and avoid areas of unsuitable flow (e.g. entrainment through water diversions), swimming capacity is an ecologically relevant index of a fishs ability to meet survival challenges. The swimming capacities of larval green sturgeon (Acipenser medirostris) and white sturgeon (A. transmontanus) had never been assessed. Therefore, we designed a study aimed to compare the ontogeny of larval green and white sturgeon (20-60 days post hatch, dph) prolonged swimming performance. Due to the differences in the stages of larval sturgeon, we swam fish in two different chambers. One chamber designed for small larval fish and another for larger larval to post-metamorphosis sub-juvenile fish. Fish were tested in 1.5 and 5.0 l calibrated swim tunnels using critical swimming velocity methodologies (Ucrit). Water velocity was increased stepwise by 5 cm/s at either 5 or 10 min intervals. Our data suggests larval sturgeons are very good swimmers soon after beginning exogenous feeding (approximately 12 dph). Our findings show that growth rate (length and mass) and eventually size at equal dph was greater for larval white sturgeon, with white sturgeon being double the greens mass by the 50-59 day interval. Results showed greater Ucrit for green sturgeon compared to white sturgeon from the beginning to the end of the larval life stage. Green sturgeon Ucrit ranged from 18.5 to 53.6 cm/s, which is approximately 30% higher than white sturgeon Ucrit, which ranged from 11.6 to 41.6 cm/s, at all age intervals. Though growth and swimming differed between the two species, the modest differences in their Ucrit likely reflects adaptations to similar water flows. Both these species have similar timing for
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spawning in the Central Valley, possibly explaining their performance similarities.
USGS, Placer Hall, 6000 J St., Sacramento CA, 95819, (916) 278-3098, lrbrown@usgs.gov
White sturgeon diet response to invasive species-mediated changes in a benthic prey assemblage
Annie Brodsky, Steven Zeug
Cramer Fish Sciences, 13300 New Airport Rd Suite 102, Auburn, CA 95602, (530) 888-1443 x15, stevez@fishsciences.net
Invasive organisms can have significant impacts on native species and the San Francisco Estuary, California (SFE) is one of the worlds most invaded estuaries. Decline of native white sturgeon (Acipenser transmontanus) in the SFE has been acknowledged, but its cause is poorly understood. Invasion by the overbite clam (Potamocorbula amurensis) drastically altered the SFE benthic prey community yet little is known about how this change has affected white sturgeon. Elucidating the response of white sturgeon diet composition to this invasion is essential to future management of the species. This study investigated the effect of the overbite clam invasion and subsequent shift in the SFE benthic prey assemblage on the feeding ecology of white sturgeon. Gut content analysis was used to compare prey composition and dietary importance between the pre- and post-invasion periods. Additionally, stable isotope analysis was employed to estimate the assimilation of prey items to sturgeon biomass in the post-invasion period. Overbite clams dominated diets in the post-invasion period accounting for > 80% of total prey volume. However, stable isotope analysis indicated this prey item contributed less to sturgeon biomass than gut contents indicated. The frequency of fish increased in the postinvasion period and isotopic analysis indicated relatively large contributions of certain fish species to sturgeon biomass. The trophic adaptability of white sturgeon has allowed them to exploit this new prey resource. However, future conservation and restoration efforts must consider a potentially destabilized food web given the large importance of a single prey item.
In 2003, a series of papers was published in San Francisco Estuary and Watershed Sciences regarding the potential role of tidal wetland restoration in improving the ecological health and water management of the San Francisco Estuary. Of particular interest was the question of whether tidal wetland restoration might enhance populations of native fishes, including species of concern such as delta smelt (Hypomesus transpacificus), longfin smelt (Spirinchus thaleichthys), Sacramento splittail (Pogonichthys macrolepidotus), and Chinook salmon (Oncorhynchus tshawytscha). At that time, there were few studies of the role of tidal wetlands with regard to fishes, so few conclusions were possible, except that new studies were needed to improve understanding of this relationship. Recent studies, including the Integrated Regional Wetland Monitoring Project, have expanded the list of fishes associated with tidal wetlands and associated nearshore habitats from 34 species in 2003 to 80 species as of 2013. Of these fishes, 22 of 28 freshwater resident species were alien but only 8 of 52 brackish/marine species were alien. Studies of trophic processes indicate that tidal marshes contribute directly to the nutrition of resident and transient fishes that access low order tidal channels and that it may be possible to create local regions where organic matter transported out of tidal marshes can contribute to the nutrition of fishes in nearby habitats. However, export of sufficient organic matter to significantly subsidize the diets of fishes inhabiting deep pelagic habitats is uncertain and will likely depend on total area restored and the geographic location of individual projects. Overall, restoring and reconnecting marsh and aquatic habitats of various kinds will likely provide multiple benefits to the estuarine ecosystem, including native fishes. A regional approach to planning and adaptive management is essential for understanding the processes determining successes and failures as tidal wetland restoration efforts move forward.
An update on the importance of tidal marshes to native fishes of the San Francisco Estuary
Larry R. Brown, Judith Drexler, Robin Stewart, Darcy Austin, and Stuart Siegel
Over the top: patterns of juvenile fish presence in flood and non-flood years
Haley Carlson, Angelica Munguia, Jasmine Shen
California Department of Water Resources, 3500 Industrial Blvd., (916)376-9850, haley.carlson@water.ca.gov
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The Yolo Bypass is a 24,000 ha engineered floodplain that has been the focus of many ecological studies. Flooding in the Yolo Bypass occurs during years of heavy rainfall primarily when the Sacramento River overtops the Fremont and Sacramento Weirs. These flood events in the bypass are able to convey up to 80% of the Sacramento River basin outflow, and it is now widely accepted that this engineered floodplain provides valuable habitat for many native fishes, especially Sacramento Splittail and juvenile Chinook Salmon. However, the amount of habitat available to fish in a given year is highly variable based on the amount of flood water that is conveyed through the bypass. In this overview, we examined how the overtopping of Fremont Weir may affect the presence or absence of juvenile fishes using the bypass. We analyzed 13 years of fish catch data (2000-2013) collected from our rotary screw trap located in the Toe Drain of the bypass. The Toe Drain is a perennial tidal channel along the east side of the bypass that maintains connectivity to the Cache Slough Complex year-round. The Toe Drain acts as a drain to floodwaters during the winter and spring, and provides a water source for local agriculture and the Yolo Wildlife Area during the summer and fall months. We separated annual data by whether Fremont Weir overtopped to compare differential patterns between juvenile fish presence and the water quality parameters: flow, secchi depth, and water temperature. We saw no significant difference in secchi depth or water temperature. As for fish catch data, in years that Fremont Weir did overtop, we saw an overall greater abundance of all juvenile fishes but an exceptional increase in presence for juvenile native species such as Chinook Salmon and Sacramento Splittail. reductions on egg incubation, fry emergence, and juvenile emigration are not well understood. Along with collaborators from the State Water Resources Control Board, the U.S. Fish and Wildlife Service, the Sacramento Water Forum, and the City of Sacramento, we assessed the impact of low flow conditions on Chinook redds on the LAR over a ten-week period following flow reductions. We used handheld GPS units to map water's edge throughout the spawning reach of the LAR at four different stream flows and overlayed this data with GPS coordinates of Chinook redd locations to quantify dewatered redds. In addition, we monitored intergravel water quality of submerged and dewatered redds. The results of this study provide information about how decreasing flows during salmonid incubation periods impact salmonid embryos. This information can be used to provide recommendations for flow management decisions in drought years that maximize benefits to salmonids while balancing other water needs.
The Passage Assessment Database, a Statewide inventory of fish passage assessments publicly available via the CalFish website
Anne Elston
Pacific States Marine Fisheries Commission, 830 S Street, Sacramento, CA 95814. (916) 327-3937, Anne.Elston@wildlife.ca.gov
Effects of flow reductions on salmonid redds and significance for juvenile salmonids
Joseph Merz, Kirsten Sellheim, Karin Dove
Cramer Fish Sciences, 3300 Industrial Blvd. Ste. 100, West Sacramento, CA, 95691, (916) 231-1681, karin.dove@fishsciences.net
The year 2013 marked the driest on record for many areas of California, with no projected changes for 2014. This drought has resulted in flow reductions to many rivers throughout the state, including the Lower American River (LAR). Flow reductions on the LAR occurred just after the peak of Chinook salmon spawning, potentially dewatering salmon redds throughout the river. The effects of these flow
The Passage Assessment Database (PAD) is an ongoing map-based inventory of known and potential barriers to fish in California. The PAD compiles currently available fish passage information from several sources, including federal, state, and local government agencies, and from non-governmental sources throughout California. The PAD is an important tool for planning and tracking the outcomes of anadromous fish passage improvement projects. For the PAD to be useful as a restoration tool, the data within the PAD need to accurately depict the on-the-ground reality of fish passage constraints, which requires that the PAD be updated regularly and available to fish passage practitioners. The PAD is publicly available via the CalFish website (www.calfish.org). CalFish, a California Cooperative Anadromous Fish and Habitat Data Program, is a multi-agency website presenting anadromous fish, stream habitat, and migration barrier data in California. The site includes standards and tools used for the collection, management, and analysis of these data.
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The poster will include an overview of the PAD, and how to access and review the barriers in the PAD, highlighting the PAD Review tool. The poster will also include information about other CalFish tools for analyzing data and CalFish datasets available, including barrier remediation reports and California Department of Fish and Wildlife priority barriers for removal. weirs have been used on rivers and streams to effectively manage and sample migratory fish populations. Resistance board weirs are currently in use throughout the Pacific Northwest; however, fishery managers outside of the United States are also starting to explore ways to utilize the technology to address their region-specific fishery questions and sample their species of interest. We describe the basic structure and function of a resistance board weir, its current fisheries management applications, and the potential to incorporate recent technological advances into resistance board weir sampling, such as spot pattern recognition, otolith microchemistry, and genetic sampling analysis.
For science! Freshwater and anadromous fish species research

Dustin Harrison, Gabriele Quillman, Sunil Rajappa, Russ Bellmer, Jamie Cary
California Department of Fish and Wildlife, Fisheries Brach, 830 S Street, Sacramento, CA 95811, (916) 445-7636, Dustin.Harrison@wildlife.ca.gov
Evidence of sturgeon distribution and habitat use in the San Joaquin River, California
Zachary J. Jackson, Jimmy R. Faukner
US Fish and Wildlife Service, 850 S Guild Avenue, Lodi, CA 95240, (209) 334-2968x408, Zachary_Jackson@fws.gov
This poster presentation synthesizes information from Scientific Collecting Permit applications collected over a two year period from 2012 to 2014. Data was analyzed to develop a comparison of types of activities and species targeted. Types of information gained and how it was used are discussed. Updates to the Scientific Collecting Permit review and valuation process are presented along with the importance of accuracy of information in the permit application and reporting requirements. Degree of differences between and among researchers in application completeness and accuracy is presented along with impacts to native fish. The value added of some of the research projects is presented along with risk to the native fish being studied. These results are discussed in the context of the variable risks and benefits to the species involved in these applied and theoretical research studies.
Resistance Board Weir A versatile fisheries management tool that can be applied worldwide
Jesse Anderson, Kyle Horvath
Cramer Fish Sciences, 3300 Industrial Blvd., Suite 100, West Sacramento, CA 95691, (209) 968-5857, anderson@fishsciences.net
For decades, fisheries managers have struggled with ways to successfully capture, enumerate, segregate, and even block migrations of anadromous fish into rivers and watersheds. In recent years, resistance board
Prior to the initiation of sturgeon field surveys in the San Joaquin River it was critical to collaborate with anglers, game wardens, and agency personnel to assess existing local knowledge and us that to inform initial sampling site selection. In 2011, this cooperative effort resulted in the first documentation of white sturgeon (Acipenser transmontanus) spawning in the San Joaquin River system. During 2012, eggs were collected from four different locations within the study area indicating that spawning occurs even during dry water years. No spawning was documented in 2013, a critical dry water year. Acoustic transmitters were implanted in adult white sturgeon during 2012 (n=10) and 2013 (n=18). Of the ten fish tagged in 2012, five returned to the capture area in 2013 suggesting that these fish may exhibit fidelity to the San Joaquin River. Three of the sturgeon during 2013 over-summered in the river and then moved out of the system in the fall during an increase in streamflow. This suggests that white sturgeon in the San Joaquin River may be more tolerant of high water temperatures than previously thought and adapted to the environmental conditions of the San Joaquin River. It remains unknown if the spawning activity that has been documented to date has resulted in viable offspring. Therefore, describing early life history survival of sturgeon in the San Joaquin River remains an active area of research. Sampling during 2014 and
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beyond is aimed at answering this question through the collection of larval or young of the year white sturgeon in the San Joaquin River.
Linkages between contaminants and sturgeon health in the San Francisco Estuary of California
Robert Bringolf, Annie Brodsky, Deke Gunderson, Zachary Jackson, Joseph Merz, Molly Webb, Steve Zeug
US Fish and Wildlife Service, 850 S Guild Avenue, Lodi, CA 95240, (209) 334-2968x408, Zachary_Jackson@fws.gov
The behavior of fall-run Chinook salmon (Oncorhynchus tshawytscha) zero, one and five days after surgical implantation of acoustic transmitters
Kristina V. Ho, Katie W. Lee, Gabriel P. Singer, Dennis E. Cocherell, Jamilynn B. Poletto, A. P. Klimley, Nann A. Fangue
University of California, Davis, Dept. of Wildlife, Fish, and Conservation Biology, One Shields Ave. Davis, CA 95616, (626) 8220811, kvho@ucdavis.edu
The San Francisco Estuary is a highly urbanized system that supports White Sturgeon (Acipenser transmontanus), an ecologically and economically important organism and the largest freshwater fish in North America. However, numerous contaminants enter the estuary in municipal and industrial sewage, and urban and agricultural runoff and their effects on acipenserid species are poorly understood. Endocrine disrupters and carcinogens (e.g., chlorinated pesticides, PCBs), linked to reduced sturgeon growth and reproduction, and elevated copper concentrations, correlated to sturgeon embryo mortality in laboratory studies, are examples of such contaminants. High selenium concentrations such as those found in the estuary food web, can be passed maternally to offspring and cause high incidence of deformities and mortality in sturgeon offspring and increased osmoregulatory stress in juvenile sturgeon. These observations illustrate the need for a greater understanding about the effects of a variety of natural (e.g., selenium, heavy metals) and unnatural compounds (e.g., triclopyr, fluridone) occurring in the Central Valley of California on native sturgeon populations. Here, we provide preliminary study results investigating relationships between contaminants in prey items and white sturgeon tissues, and observed histological abnormalities of adult white sturgeon in the San Francisco Estuary.
Acoustic transmitters are powerful monitoring tools used to assess spatial distribution patterns of wideranging species that cannot be directly followed through radio telemetry. Monitoring methodologies are critical for aquatic species that are in decline due to anthropogenic alterations to the environment. Chinook salmon (Oncorhynchus tshawytscha), regarded for their economic value and ecosystem services, are being studied using acoustic telemetry to gain insights into additional causes of their diminishing wild populations and poor outmigration rates. However, few studies compare the differences in behavior between acoustically tagged and non-tagged fish or investigate behavioral changes as a function of the length of recovery following transmitter implantation. This is a concern because tagged individuals may not behave in a manner representative of the fish population in the watershed, yielding unreliable field monitoring results. We tested fall-run Chinook behavior zero, one, and five days after surgical implantations of JSATs transmitters (Model SS300; mean weight = 300 mg). Individual fish (non-tagged mean total length = 15.72 cm; tagged mean total length = 17.25 cm) were placed in a latency behavioral box (LBB) with a retractable door that opened after an initial acclimation period (15 min). The time to initial and final emergence from the LBB was recorded as an index of boldness and shyness for tagged and control fish. Results showed that O. tshawytscha that have been allowed a five day recovery period emerged from the LBB 93% of the time, which was as bold as their non-tagged counterparts, while tagged fish without a recovery period only left the LBB approximately half of the time. These data show that tag implantation influences fish behavior and suggest that tagging procedures should consider surgical recovery times and acclimation to the transmitters weight for resumption of normal fish behavior.
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Developing a SNP panel for genetic management of Delta smelt (Hypomesus transpacificus)
Ryan M. Lew, Mariah H. Meek, Amanda J. Finger, Melinda R. Baerwald, Alisha Goodbla, Bernie May
Department of Animal Science, University of California Davis, 1 Shields Avenue, Davis, CA 95616, (415) 710-5974, rmlew@ucdavis.edu
Use of video cameras in monitoring

Katrina Martens
Cramer Fish Sciences, 3300 Industrial Blvd., Suite 100 West Sacramento, CA 95691, (916) 231-1681 x1, Katrina.martens@fishsciences.net
Since 2008, the Fish Conservation and Culture Laboratory (FCCL) has raised a captive-bred population of Delta smelt (Hypomesus transpacificus) as a refuge to safeguard against extirpation in the San Francisco Estuary. In conjunction with the FCCL, the Genomic Variation Laboratory of UC Davis has genetically managed this population to be genetically similar to the wild population to ensure preservation of standing genetic diversity. We created a panel of single nucleotide polymorphisms (SNP) to augment the microsatellite panel currently in use to genotype fish and assign parentage. Properly implemented, a SNP panel is a more powerful and repeatable method for high-throughput genotyping. This streamlines genetic management, which is performed in real-time during the spawning season. For the SNP discovery, we sequenced 27 individuals of the 2012 broodstock using restriction-site associated DNA sequencing (RAD-seq), yielding 2317 new SNPs. To develop a linkage map to facilitate identification of effective SNP markers for a genotyping panel, we used RAD-seq to genotype three single pair crosses and 46 offspring per family at the 2317 discovered loci. We successfully mapped 1124 loci and identified 26 linkage groups. This information was then used to select 104 loci as candidates for assay development based on minor allele frequency (>20%), neutrality (Hardy-Weinberg equilibrium), and marker location. We evaluated our assays on a 96x96 Integrated Fluidic Circuit (Fluidigm EP1). 18 individuals from the RAD-seq study were re-genotyped with the assays to test marker accuracy. We also genotyped 76 samples of known parent-offspring relationship to assess the panels ability to assign parentage using the program CERVUS 3.0. We found that a panel of 24 independent SNPs, chosen from the 96 total based on the highest minor allele frequency, could successfully assign parents and offspring if each individual used in the analysis was genotyped at a minimum of 18 loci.
Video cameras are commonly used as a tool to monitor organism behavior; however, the use of underwater video has become more prevalent in recent years for fisheries applications as video cameras have become smaller, higher resolution, more cost-effective, and more customizable. Stationary video cameras coupled with other passive monitoring equipment (i.e., infrared, sonar, electronic counters, etc.) have become commonplace for use at resistance board weirs, passageways, and fish ladders. Sites with direct power have the luxury of connecting high-resolution video cameras to computers, digital video recorders (DVR), and motion detection software to reduce user review time. This poster describes applications, and challenges, of underwater video as a technique to quantify and observe aquatic organisms in riverine habitats. We describe several studies that have used video technology to quantify salmonids and non-native predators, document spawning activity of an endangered fish species, and experimentally test utilization of habitat structures by juvenile salmonids within habitat restoration sites. These studies have implications for both short- and long-term monitoring efforts and for habitat restoration project design.
Tag retention and health of Juvenile Chinook salmon (Oncorhynchus tschawytscha) implanted with radio transmitters: Implications for survival and migration studies
Katherine McElroy, Clark Watry
University of California, Santa Cruz 137 Cayuga Street Santa Cruz, CA 95062, (760) 522-0263, katiemcelroy1206@gmail.com
Miniature acoustic and radio transmitters have opened new areas of investigation for fisheries researchers.
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These tags provide a means to collect more detailed data on the survival, movement, and behavior of individual fish, at a smaller size, than other techniques. However, since these transmitters are surgically implanted into the body cavity of individual fish, it is important to provide an accurate representation of post-operative survival, tag retention rate, and potential adverse effects resulting from the tagging process when conducting survival and behavior studies. Failure to take these components into account may alter study results. In the spring of 2013, we performed a juvenile Chinook salmon survival and migration study on the lower Stanislaus River using radio nano-transmitters (0.25 g) with external antennas. We performed a twotier laboratory experiment to: 1) assess post-operative survival, tag retention, and behavioral recovery; and, 2) evaluate post-recovery condition. We conducted controlled monitoring using a subset of study fish selected for treatment (i.e., tagged) and control (i.e., no tag) groups. We randomly selected 40 representative fish, split equally among the treatment (n = 20) and control (n = 20) groups, for each release event (Group 1 and Group 2). Control fish were selected and transported in a similar manner to treatment fish except they were not subject to anesthetization, handling, or tag implantation. A submersible video camera was mounted inside study tanks to collect video footage during each of two different three-week monitoring periods to analyze behavior of tagged and un-tagged fish. Following the second 3-week monitoring period, we evaluated fish from both groups for tag retention, growth and general health. We will present results from this study and discuss potential implications for introducing bias in survival and migration study results. coho salmon recovery plan with the primary purpose of accomplishing one or more of the following: (1) The removal of a road crossing and/or the replacement of a culvert that is a barrier to fish movement up and down stream; (2) The restoration of eroded or denuded streambanks using predominantly nonrock bioengineering practices and the revegetation of stream corridors with native species; and (3) Large Wood Material (LWM) treatments designed to create or enhance fish habitat and/or increase stream complexity. For more information, the project request form and instruction pages please visit https://www.dfg.ca.gov/fish/Resources/Coho/HELP.
Fecundity of the Tidewater goby in captive versus wild populations

Lana Ray
Humboldt State University, 1895 H St, Apt 29, Arcata, CA 95521, (951) 454-6458, Lana.m.ray@gmail.com
The tidewater goby is a small benthic marine fish with habitat preferences for lagoons, marshes, creeks and estuaries. It is an annual species that rarely exceeds 50 mm SL. This species is threatened by habitat loss and degradation (e.g. development of coastal wetlands, water diversions, and stream channelization), and predation by exotic fishes. Fewer than fifty (of the original 134) populations remained as of 1990, prompting the U.S. Fish and Wildlife Service to list the tidewater goby as a federally endangered species in 1994. Understanding the tidewater gobys feeding habits is a critical component for developing a recovery program. Diet studies can identify major prey, which may be restricted to certain habitats or be sensitive to habitat disruption or pollutants. On the other hand, knowledge of feeding habits might reveal adaptability to diverse prey resources. The diet of the tidewater goby consists primarily of crustaceans, dipteran larvae, gastropods, and invertebrate eggs. The overall diet varies, however, both seasonally and spatially. Recovery efforts will involve identification and protection of critical habitat and possibly reintroductions of the species to other estuaries. There have been only a couple fecundity studies on the tidewater goby. Tidewater gobies are iteroparous and have relatively high, length dependent fecundities. I will
California Department of Fish and Wildlife Coho salmon Habitat Enhancement Leading to Preservation (HELP)
Mary Olswang
California Department of Fish and Wildlife , Fisheries Branch, 830 S Street, Sacramento, CA 95816, (916) 445-7633, mary.olswang@wildlife.ca.gov
On January 1, 2013, the Coho Salmon Habitat Enhancement Leading to Preservation Act, or Coho HELP Act, went into effect. Coho HELP is a CDFW permitting alternative for anyone interested in developing and installing small coho salmon habitat enhancement project, defined as a restoration project in a region described in an adopted state or federal
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investigate the fecundity on the tidewater goby Eucyclogobius newberryi held in captivity. Previous studies have shown the tidewater goby have a varied diet, we fed our experimental population only frozen Artemia daily and live Artemia once. I believe that a continuous supply of unaltering food type will affect the overall fecundity in captive females. benefits of flow management and specific types of habitat restoration can readily be estimated with the model.
A place to call home: A synthesis of Delta Smelt habitat in the upper San Francisco Estuary
Ted Sommer
California Department of Water Resources, 3500 Industrial Blvd, West Sacramento CA 95691-6521, (916) 376-9772, Ted.Sommer@water.ca.gov
Determining the habitat bottleneck is it rearing or spawning limited?

Jared Siegel, Steve Cramer, Kevin Ceder, Kirsten Selheim
Cramer Fish Sciences, 3300 Industrial Blvd., Suite 100, West Sacramento, CA 95691, (916) 231-1681, jared.siegel@fishsciences.net
Biologists confronted with prescribing minimum flows or choosing which habitat restoration projects get funding have wrestled with the challenge of identifying which habitat factors are the real bottleneck to fish production. We identified relationships between measurable habitat features and fish preferences for rearing and spawning, based on published studies. Rearing capacity is influenced by channel unit type, depth, cover, area, fine sediment, and temperature, while spawning capacity is influenced by depth and area of suitable gravels. We developed methods to measure all of these features on a single survey during base flow, and then predict how the features would differ at the different flows expected in different seasons. We field tested these methods to estimate production potential of spring Chinook, steelhead, and resident rainbow trout in Battle Creek, a high gradient boulderdominated stream. The factor that was most limiting was strongly affected by the season in which spawning occurs for each species and the size of the spawners. Spring Chinook spawn during summer base-flow, while steelhead and rainbow trout spawn during winterspring high flows. Rearing capacity for the juveniles of both species is constrained by summer low flows. The number of suitable patches for steelhead spawning was substantially greater than for Chinook, because steelhead require half of depth required by Chinook (15 cm vs. 30 cm), and the area defended per spawning pair is only 4 m2 for steelhead, one fifth of the 20.7 m2 required per pair of Chinook. These methods clearly distinguished that spawning capacity was most limiting for spring Chinook, while rearing capacity was most limiting for steelhead and rainbow trout. Potential
We used a combination of published literature and field survey data to synthesize the available information about habitat use by Delta Smelt Hypomesus transpacificus, a declining native species in the San Francisco Estuary. Management of this species is currently an issue of national importance because its distribution overlaps with the water supply for 8 percent of the United States population. Delta Smelt habitat ranges from San Pablo and Suisun bays to their freshwater tributaries, including the Sacramento and San Joaquin Delta. In recent years, substantial numbers of Delta Smelt have colonized tidal freshwater habitat in Liberty Island, a north Delta area that flooded in 1997. The species has more upstream distribution during spawning as opposed to juvenile rearing periods. Postlarvae and juveniles tend to have a more downstream distribution during wetter years. Delta Smelt are most common in low salinity habitat (<6 psu) with high turbidities (>12 ntu) and moderate temperatures (7-25 C). They do not appear to have strong substrate preferences, but sandy shoals are important for spawning in other osmerids. The evidence to date suggests that they generally require at least some tidal flow in their habitats. Delta Smelt also occur in a wide range of channel sizes, although they seem to be rarer in small channels (<15 m wide). Nonetheless, there is some evidence that open water adjacent to habitats with long water residence times (e.g. tidal marsh, shoal, low order channels) may be favorable. Other desirable features of Delta Smelt habitat include high calanoid copepod densities and low levels of submerged aquatic vegetation and the toxic algae Microcystis.
Enhancing secondary production through gravel augmentation on regulated rivers

Jamie Sweeney 73

Cramer Fish Sciences, 3300 Industrial Blvd STE 100 West Sacramento, CA 95691, (916) 231-1681, Jamie.Sweeney@fishsciences.net
There has been an increase in gravel augmentation projects on regulated California Central Valley rivers in response to anthropogenic influences (e.g. dams, diversions, agriculture, levees and urban development) that reduce the quantity and quality of bed sediment substrate. Although gravel augmentation is generally aimed at supplying substrate of appropriate size for spawning salmonids, it may also influence other important river ecosystem processes. For example, aquatic macroinvertebrate production may be sensitive to both anthropogenic disturbance and gravel augmentation. Aquatic macroinvertebrates play a pivotal role in river ecosystem functioning and many invertebrate taxa demonstrate an affinity for particular substrate sizes. Aquatic macroinvertebrates are an essential prey source for juvenile salmonids, and several studies have demonstrated that juvenile salmonids display dietary preferences for particular taxa. Therefore, incorporating the substrate size preferences of key macroinvertebrate prey taxa into gravel augmentation projects may enhance prey production. We examined the effect of gravel augmentation on the colonization and composition of aquatic macroinvertebrates by comparing density, biomass and community composition among three different gravel sizes (small, medium and large) in a gravel augmented area on the Lower American River. Our observations show that large gravel produced significantly higher macroinvertebrate density, which suggests that larger gravel may support increased forage production for juvenile salmonids. This study demonstrates that gravel augmentation projects designed to improve adult salmonid spawning habitat can also improve ecosystem functions and increase secondary productivity, which may benefit juvenile salmonid life stages as well.
Central Valley. In an effort to develop the relationship between discharge and floodplain inundation, the U.S. Fish and Wildlife Service developed a two-dimensional hydraulics model withSRH-2D. Determination of floodplain inundation threshold was performed by identifying inflection points in wetted area versus discharge plots. We shared the model with local irrigation districts. The Districts reviewed the model and created a new model, improving on the original design by successfully calibrating the model for two floodplaininundating flow events, using high-resolution spatial analyses to quantify inundated area, and greatly reducing the model run time. We reviewed the new model and suggested a process for further refinement of the definition of floodplain inundated area which resulted in agreement between the parties to move forward in multiple venues with the modified new model. Success! We have avoided competing model paralysis.
Potential for tag collisions and false negatives in fish with multiple PIT tags present following predation events
Veronica Wunderlich
California Department of Water Resources, Bay-Delta Office, 1416 Ninth Street, Room 115, Sacramento, California 95814, (916) 6574243, vwunderl@water.ca.gov
Avoiding model wars: How we got to a mutually agreed-upon floodplain versus flow solution
JD Wikert, Mark Gard, Paul Frank
U.S. Fish and Wildlife Service, 850 S. Guild Avenue, Lodi, CA 95242, (209) 403-1046, john_wikert@fws.gov
Passive integrated transponder (PIT) tags are commonly used in fisheries research throughout the Delta for a wide variety of fish species, presenting the potential for multiple tags to occur within the same fish in the case of predation events. To investigate the potential of tag collisions resulting from multiple tags, we conducted a series of controlled experiments simulating from 1 to 5 tags in a single fish in a variety of orientations. Depending upon the orientation and relative proximity to the PIT tag reader, it is possible to miss existing tags within a scanned fish, and to experience false negatives when multiple tags are present. A systematic approach to scanning fish, in addition to a secondary marking protocol, can help avoid these false negatives in the field.
Several ongoing processes are currently attempting to set flow schedule in the Stanislaus River in Californias
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2014 AFS Cal-Neva 48th Annual Conference Program

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2014 AFS Cal-Neva 48th Annual Conference Program

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California-Nevada Chapter of the American Fisheries Society

48TH ANNUAL CONFERENCE MARCH 27 29, 2014

Embassy Suites Sacramento Riverfront Promenade

Saturday Morning Technical Sessions

Saturday Afternoon Technical Sessions

Oral Presentation Abstracts Poster Presentation Abstracts

CAL-NEVA 48TH ANNUAL CONFERENCE.

Poster Session - Welcome Social, Job Fair, and Vendor Show

Vendor Set-up and Display

Student Social (everyone is welcome)

Continuing Education Sessions

Friday, March 28, 2014

Chapter Business Lunch Meeting

Welcome & Plenary Session: Challenges. Collaboration. Solutions.

7:00pm 12:00am Old Sacramento Ballroom

Saturday, March 29, 2014

8:00am 10:00am Atrium

Afternoon Technical Sessions

Morning Technical Sessions

CHALLENGES. COLLABORATION. SOLUTIONS.

Challenges. Collaboration. Solutions.

CAL-NEVA 48TH ANNUAL CONFERENCE.

CHALLENGES. COLLABORATION. SOLUTIONS.

CAL-NEVA 48TH ANNUAL CONFERENCE.

CHALLENGES. COLLABORATION. SOLUTIONS.

Student Job Fair Student-Mentor Lunch

Student Paper and Poster Competition

Annual Business Meeting

CAL-NEVA 48TH ANNUAL CONFERENCE.

Collaboration and multidisciplinary science: reflections from a junior faculty member

Christina (Tina) Swanson, Ph.D.

CHALLENGES. COLLABORATION. SOLUTIONS.

David J. Manning, M.S.

Jeffrey McLain, M.S.

Collaborating in the California agency melting pot: coping and solutions

CHALLENGES. COLLABORATION. SOLUTIONS.

In the dance between science and policy, who leads?

CAL-NEVA 48TH ANNUAL CONFERENCE.

Introduction to Genetics Monitoring

CHALLENGES. COLLABORATION. SOLUTIONS.

Section 10 and 4(d) Rule

CAL-NEVA 48TH ANNUAL CONFERENCE.

CHALLENGES. COLLABORATION. SOLUTIONS.

Morning Plenary Session

Welcome & Plenary Session: Challenges. Collaboration. Solutions.

Collaboration and multidisciplinary science: reflections from a junior faculty member

10:00am 10:30am 10:30am 10:50am

BREAK Jeff McLain

Collaborating in the California agency melting pot: coping and solutions

In the dance between science and policy, who leads?

CAL-NEVA 48TH ANNUAL CONFERENCE.

Afternoon Technical Sessions

Session I: Hydroacoustic Symposium

Jacqueline Pearson-Meyer Melinda Molnar

CHALLENGES. COLLABORATION. SOLUTIONS.

Afternoon Technical Sessions

Session II: Dam Removal and Water Quality

4:00pm 4:20pm 4:20pm 4:40pm

Chris Hammersmark Stephen Louie

CAL-NEVA 48TH ANNUAL CONFERENCE.

Afternoon Technical Sessions

Sessions I & II: Challenges, Collaboration, and Solutions in FERC Relicensing

2:20pm 2:40pm 2:40pm 3:00pm

Management of the spring snowmelt recession in regulated systems