NOAA FISHERIES

The origins of the anomalous warming in the California coastal ocean and San Francisco Bay during 2014-2016 Chao, Yi, John D. Farrara, Eric Bjorkstedt, Fei Chai, Francisco Chavez, Daniel L. Rudnick, Wendy Enright, Jennifer L. Fisher, William T. Peterson, Gregory F. Welch, Curtiss O. Davis, Richard C. Dugdale, Frances P. Wilkerson, Hongchun Zhang, Yinglong Zhang, and Eli Ateljevich Journal of Geophysical Research: Oceans 122(9):7537-7557

Readying California fisheries for climate change Chavez, Francisco P., Christopher Costello, Debbie Aseltine-Neilson, Holly Doremus, John Field, Steve Gaines, Madeleine Hall-Arber, Nathan Mantua, Carrie Pomeroy, Leila Sievanen, Bill Sydeman, Barry Wayne-McCovey Jr., and Sara Wheeler (Climate Change and Fisheries Working Group) California Ocean Science Trust, Oakland, California. 58 p.

State of deep-sea coral and sponge ecosystems of the U.S. West Coast Clarke, M. Elizabeth, Curt E. Whitmire, and Mary M. Yoklavich In: Thomas F. Hourigan, Peter J. Etnoyer, and Stephen D. Cairns (eds.), The state of deep-sea coral and sponge ecosystems of the United States, p. 113-155. NOAA Technical Memorandum NMFS-OHC-4.

Mobile acoustic sampling to map bathymetry and quantify the densities and distributions of salmonid smolt predators in the San Joaquin River Cutter, G.R. Jr., S.C. Manugian, J. Renfree, J. Smith, C. Michel, D. Huff, T.S. Sessions, B.E. Elliot, K. Stierhoff, S. Mau, D. Murfin, and D.A. Demer U.S. Department of Commerce, NOAA Technical Memorandum NMFS-SWFSC-575. 134 p.

Identification of multiple genetically distinct populations of Chinook salmon (Oncorhynchus tshawytscha) in a small coastal watershed Davis, Chante D., John Carlos Garza, and Michael A. Banks Environmental Biology of Fishes 100(8):923-933

Life history effects on hatchery contributions to ocean harvest and natural-area spawning Davison, Raziel J., and William H. Satterthwaite Canadian Journal of Fisheries and Aquatic Sciences 74(10):1575-1587

Large batoid fishes frequently consume stingrays despite skeletal damage Dean, Mason N., Joseph J. Bizzarro, Brett Clark, Charlie J. Underwood, and Zerina Johanson Royal Society Open Science 4(9):170674 (11 p.)

Bias in estimation of biological reference points when three-parameter stock-recruit relationships are considered appropriate: An extension of the results of Mangel et al. 2013 Dick, E.J., and Nick Grunloh In: Report of the Groundfish Productivity Workshop of the Pacific Fishery Management Council's Scientific and Statistical Committee (NOAA Fisheries, Alaska Fisheries Science Center, Seattle, Washington, December 6-8, 2016), p. 8-9. March 2017 Briefing Book, Agenda item I.2, Attachment 2. Pacific Fishery Management Council, Portland, Oregon.

Depletion-based stock reduction analysis (DB-SRA) for starry flounder (Platichthys stellatus) in U.S. waters off California, Oregon and Washington Dick, E.J., Jim Hastie, Patrick Mirick, and Tien-shui Tsou In: November 2017 Briefing Book, Agenda Item F.6, Attachment 3. Pacific Fisheries Management Council, Portland, Oregon. 14 p.

A meta-analysis of fecundity in rockfishes (genus Sebastes) Dick, E.J., Sabrina Beyer, Marc Mangel, and Stephen Ralston Fisheries Research 187:73-85

Natural history observations of Hawaiian garden eels, Gorgasia hawaiiensis (Congridae: Heterocongrinae), from the island of Hawai'i Donham, Emily, Michael S. Foster, Marc R. Rice, Gregor M. Cailliet, Mary M. Yoklavich, and Scott L. Hamilton Pacific Science 71(2):135-147

Ecosystem effects of invertebrate fisheries Eddy, Tyler D., Heike K. Lotze, Elizabeth A. Fulton, Marta Coll, Cameron H. Ainsworth, Julio Neves de Araujo, Catherine M. Bulman, Alida Bundy, Villy Christensen, John C. Field, Neil A. Gribble, Mejs Hasan, Steve Mackinson, and Howard Townsend Fish and Fisheries 18(1):40-53

Evaluating economic efficiency of a water buyback program: The Klamath irrigation project Elbakidze, Levan, Benjamin Fa'anunu, Aaron Mamula, and R. Garth Taylor Resource and Energy Economics 48:68-82

How are warm and cool years in the California Current related to ENSO? Fiedler, Paul C., and Nathan J. Mantua Journal of Geophysical Research: Oceans 122(7):5936-5951

Yelloweye rockfish Stock Assessment Review (STAR) Panel report Field, John, Kevin Stokes, Panayiota Apostolaki, and John Budrick Pacific Fishery Management Council, Portland, Oregon. 15 p.

Yellowtail rockfish Stock Assessment Review (STAR) Panel report Field, John, Kevin Stokes, Panayiota Apostolaki, and John Budrick Pacific Fishery Management Council, Portland, Oregon. 25 p.

The buffer value of groundwater when well yield is limited Foster, T., N. Brozovic, and C. Speir Journal of Hydrology 547:638-649

Restoring rivers and floodplains: Hydrology and sediments as drivers of change Friberg, Nikolai, Lee Harrison, Mathew O'Hare, and Desiree Tullos Ecohydrology 10(5):e1884 (3 p.)

Improving catch estimation methods in sparsely sampled mixed-stock fisheries Grunloh, Nick, Edward Dick, Don Pearson, John Field, and Marc Mangel In: September 2017 Briefing Book, Agenda Item E.3, Attachment 1. Pacific Fisheries Management Council, Portland, Oregon. 5 p.

Species-specific responses of juvenile rockfish to elevated pCO2: from behavior to genomics Hamilton, Scott L., Cheryl A. Logan, Hamilton W. Fennie, Susan M. Sogard, James P. Barry, April D. Makukhov, Lauren R. Tobosa, Kirsten Boyer, Christopher F. Lovera, and Giacomo Bernardi PLoS ONE 12(1):e0169670 (23 p.)

Coupled geomorphic and habitat response to a flood pulse revealed by remote sensing Harrison, Lee R., Andrew Pike, and David A. Boughton Ecohydrology 10(5):e1845 (13 p.)

California Current Integrated Ecosystem Assessment (CCIEA): California Current Ecosystem status report, 2017 Harvey, Chris, and Toby Garfield (eds.) A report of the NOAA CCIEA Team to the Pacific Fishery Management Council. 63 p.

Ecosystem status report of the California Current for 2017: a summary of ecosystem indicators compiled by the California Current Integrated Ecosystem Assessment Team (CCIEA) Harvey, Chris, Newell Garfield, Gregory Williams, Kelly Andrews, Caren Barcelo, Katie Barnas, Steven Bograd, Richard Brodeur, Brian Burke, Jason Cope, Lynn deWitt, John Field, Jennifer Fisher, Correigh Greene, Thomas Good, Elliott Hazen, Daniel Holland, Michael Jacox, Stephen Kasperski, Su Kim, Andrew Leising, Sharon Melin, Cheryl Morgan, Stuart Munsch, Karma Norman, William T. Peterson, Melissa Poe, Jameal Samhouri, Isaac Schroeder, William Sydeman, Julie Thayer, Andrew Thompson, Nick Tolimieri, Anna Varney, Brian Wells, Thomas Williams, and Jeannette Zamon U.S. Department of Commerce, NOAA Technical Memorandum NMFS-NWFSC-139. 52 p.

Testing the effects of manipulated predator densities and environmental variables on juvenile salmonid survival in the lower San Joaquin River Hayes, Sean, David Huff, David Demer, Cyril Michel, George (Randy) Cutter, Nick Demetras, Brendan Lehman, Suzanne Manugian, Steve Lindley, Joseph Smith, Thomas Quinn, Jacob McQuirk, Mike Cane, Marty Gingras, and Mike Harris Report prepared for California Department of Water Resources, Bay-Delta Office, Temporary Barriers and Lower San Joaquin, Agreement no. 4600010100. 266 p.

Effects of recruitment variability and fishing history on estimation of stock-recruit relationships: Three case studies from U.S. West Coast fisheries He, Xi, and John Field In: Report of the Groundfish Productivity Workshop of the Pacific Fishery Management Council's Scientific and Statistical Committee (NOAA Fisheries, Alaska Fisheries Science Center, Seattle, Washington, December 6-8, 2016), p. 14-15. March 2017 Briefing Book, Agenda item I.2, Attachment 2. Pacific Fishery Management Council, Portland, Oregon.

NMFS Southwest Fisheries Science Center: Agency report to the Technical Subcommittee of the Canada-U.S. Groundfish Committee He, Xi, and John Field (eds.), Aaron Mamula, Susan Sogard, Andrew Thompson, Nick Wegner, and Mary Yoklavich In: Report of the Technical Subcommittee of the Canada-United States Groundfish Committee: 58th annual meeting of the TSC (April 25-26, 2017, Juneau, Alaska), p. 362-385. Pacific States Marine Fisheries Commission.

Model description for the Sacramento River winter-run Chinook salmon life cycle model Hendrix, Noble, Eva Jennings, Anne Criss, Eric Danner, Vamsi Sridharan, Correigh M. Greene, Hiroo Imaki, and Steven T. Lindley NOAA Southwest Fisheries Science Center, Fisheries Ecology Division, Santa Cruz, California. 51 p.

Improved fisheries management through life stage monitoring: The case for the southern Distinct Population Segment of North American green sturgeon and the Sacramento-San Joaquin River white sturgeon Heublein, Joseph, Russ Bellmer, Robert D. Chase, Phaedra Doukakis, Marty Gingras, Douglas Hampton, Joshua A. Israel, Zachary J. Jackson, Rachel C. Johnson, Olaf P. Langness, Sean Luis, Ethan Mora, Mary L. Moser, Larissa Rohrbach, Alicia M. Seesholtz, and Ted Sommer U.S. Department of Commerce, NOAA Technical Memorandum NMFS-SWFSC-588. 35 p.

Life history and current monitoring inventory of San Francisco Estuary sturgeon Heublein, Joseph, Russ Bellmer, Robert D. Chase, Phaedra Doukakis, Marty Gingras, Douglas Hampton, Joshua A. Israel, Zachary J. Jackson, Rachel C. Johnson, Olaf P. Langness, Sean Luis, Ethan Mora, Mary L. Moser, Larissa Rohrbach, Alicia M. Seesholtz, Ted Sommer, and Jeffrey S. Stuart U.S. Department of Commerce, NOAA Technical Memorandum NMFS-SWFSC-589. 39 p.

El Nino episodes coincide with California moray Gymnothorax mordax settlement around Santa Catalina Island, California Higgins, B.A., D. Pearson, and R.S. Mehta Journal of Fish Biology 90(4):1570-1583

Impact of catch shares on diversification of fishers' income and risk Holland, Daniel S., Cameron Speir, Juan Agar, Scott Crosson, Geret DePiper, Stephen Kasperski, Andrew W. Kitts, and Larry Perruso Proceedings of the National Academy of Sciences of the United States of America 114(35):9302-9307

Chinook salmon smolt mortality zones and the influence of environmental factors on out-migration success in the Sacramento River Basin Iglesias, Ilysa S., Mark J. Henderson, Cyril J. Michel, Arnold J. Ammann, and David D. Huff Prepared for U.S. Fish and Wildlife Service, Anadromous Fish Screen Program, Sacramento, California. 30 p.

Science advancements key to increasing management value of life stage monitoring networks for endangered Sacramento River winter-run Chinook Salmon in California Johnson, Rachel C., Sean Windell, Patricia L. Brandes, J. Louise Conrad, John Ferguson, Pascale A.L. Goertler, Brett N. Harvey, Joseph Heublein, Joshua A. Israel, Daniel W. Kratville, Joseph E. Kirsch, Russell W. Perry, Joseph Pisciotto, William R. Poytress, Kevin Reece, and Brycen G. Swart San Francisco Estuary and Watershed Science 15(3):1 (41 p.)

Klamath River fall Chinook salmon age-specific escapement, river harvest, and run size estimates, 2016 run Klamath River Technical Team Klamath River Technical Team. 24 p.

Ocean abundance projections and prospective harvest levels for Klamath River fall Chinook, 2017 season Klamath River Technical Team Klamath River Technical Team. 30 p.

Real-time nodes permit adaptive management of endangered species of fishes Klimley, A. Peter, Thomas V. Agosta, Arnold J. Ammann, Ryan D. Battleson, Matthew D. Pagel, and Michael J. Thomas Animal Biotelemetry 5:22 (15 p.)

Geographic concentration of the Atlantic sea scallop fishery Lee, Min-Yang, Cameron Speir, Andrew Carr-Harris, and Sharon Benjamin Review of Regional Studies 47:25-46

Developmental order of a secondary sexual trait reflects gonadal development in male sheepshead minnows (Cyprinodon variegatus) Lee, Who-Seung, Marc Mangel, and Stephan B. Munch Evolutionary Ecology Research 18(5):531-538

Relationships between Chinook Salmon swimming performance and water quality in the San Joaquin River, California Lehman, Brendan, David D. Huff, Sean A. Hayes, and Steven T. Lindley Transactions of the American Fisheries Society 146(2):349-358

Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout (Oncorhynchus mykiss) in the San Francisco Bay Area: application of adaptive genomic variation to conservation in a highly impacted landscape Leitwein, Maeva, John Carlos Garza, and Devon E. Pearse Evolutionary Applications 10(1):56-67

Size-conditional smolting and the response of Carmel River steelhead to two decades of conservation efforts Lopez Arriaza, Juan, David A. Boughton, Kevan Urquhart, and Marc Mangel PLoS ONE 12(11):e0188971 (23 p.)

Anthropogenic noise generated by mobile vehicles used to survey rockfishes in the Channel Islands, California [abstract] Madrigal, Brijonnay, Alison K. Stimpert, Mary M. Yoklavich, and W. Waldo Wakefield Journal of the Acoustical Society of America 141(5):3865

Phenomenological vs. biophysical models of thermal stress in aquatic eggs Martin, Benjamin T., Andrew Pike, Sara N. John, Natnael Hamda, Jason Roberts, Steven T. Lindley, and Eric M. Danner Ecology Letters 20(1):50-59

Integrating lipid storage into general representations of fish energetics Martin, Benjamin T., Ron Heintz, Eric M. Danner, and Roger M. Nisbet Journal of Animal Ecology 86(4):812-825

Spatial valuation of California marine fisheries as an ecosystem service Miller, Rebecca R., John C. Field, Jarrod A. Santora, Melissa H. Monk, Rosemary Kosaka, and Cynthia Thomson Canadian Journal of Fisheries and Aquatic Sciences 74(11):1732-1748

Evaluation of alternative marking/tagging systems for hatchery produced California fall-run Chinook salmon Mohr, Michael S., William H. Satterthwaite, David G. Hankin, Peter A. Bisson, Churchill B. Grimes, Scott Hamelberg, David C. Hillemeier, Steven T. Lindley, Alice Low, Melodie L. Palmer-Zwahlen, Jim Smith, and Thomas H. Williams U.S. Department of Commerce, NOAA Technical Memorandum NMFS-SWFSC-571. 57 p.

Abundance and distribution of sturgeon feeding pits in a Washington estuary Moser, Mary L., Kim Patten, Stephen C. Corbett, Blake E. Feist, and Steven T. Lindley Environmental Biology of Fishes 100(5):597-609

Avoiding a crisis of motivation for ocean management under global environmental change Mumby, Peter J., James N. Sanchirico, Kenneth Broad, Michael W. Beck, Peter Tyedmers, Megan Morikawa, Thomas A. Okey, Larry B. Crowder, Elizabeth A. Fulton, Denny Kelso, Joanie A. Kleypas, Stephan B. Munch, Polita Glynn, Kathryn Matthews, and Jane Lubchenco Global Change Biology 23(11):4483-4496

Circumventing structural uncertainty: A Bayesian perspective on nonlinear forecasting for ecology Munch, Stephan B, Valerie Poynor, and Juan Lopez Arriaza Ecological Complexity 32B:134-143

Meta-analysis comparing parametric and non-parametric stock-recruit models Munch, Steve In: Report of the Groundfish Productivity Workshop of the Pacific Fishery Management Council's Scientific and Statistical Committee (NOAA Fisheries, Alaska Fisheries Science Center, Seattle, Washington, December 6-8, 2016), p. 12-14. March 2017 Briefing Book, Agenda item I.2, Attachment 2. Pacific Fishery Management Council, Portland, Oregon.

Fisheries economics of the United States, 2015 National Marine Fisheries Service NOAA Technical Memorandum NMFS-F/SPO-170. 245 p.

Out-migration survival of wild Chinook salmon (Oncorhynchus tshawytscha) smolts from Mill Creek through the Sacramento River during drought conditions Notch, Jeremy Master's thesis, University of California, Santa Cruz. 81 p.

Preliminary evaluation of alternative Sacramento River winter Chinook salmon control rules O'Farrell, Michael R. In: April 2017 Briefing Book, Agenda Item E.1.a, SRWCW Report 1 (14 p.). Pacific Fishery Management Council, Portland, Oregon.

Sacramento River winter Chinook management strategy evaluation: methods supplement O'Farrell, Michael R. In: April 2017 Briefing Book, Agenda Item E.1.a, SRWCW Report 2 (14 p.). Pacific Fishery Management Council, Portland, Oregon.

ENSO impacts on ecosystem indicators in the California Current System Ohman, Mark D., Nate Mantua, Julie Keister, Marisol Garcia-Reyes, and Sam McClatchie US CLIVAR Variations 15(1):8-15

Evaluation of Sacramento River winter Chinook salmon control rules: updated Management Strategy Evaluation analysis Pacific Fishery Management Council (Ad Hoc Sacramento River Winter Chinook Workgroup) In: September 2017 Briefing Book, Agenda Item F.2.a, SRWCW Report 1 (24 p.). Pacific Fishery Management Council, Portland, Oregon.

Further evaluation of Sacramento River winter Chinook salmon control rules: addendum to Ad Hoc SRWC Workgroup (2017) Pacific Fishery Management Council (Ad Hoc Sacramento River Winter Chinook Workgroup) In: November 2017 Briefing Book, Agenda Item D.3.a, SRWCW Report 1 (9 p.). Pacific Fishery Management Council, Portland, Oregon.

Review of 2016 ocean salmon fisheries: Stock assessment and fishery evaluation document for the Pacific Coast Salmon Fishery Management Plan Pacific Fishery Management Council (Salmon Technical Team) Pacific Fishery Management Council, Portland, Oregon. 342 p.

Preseason report I: Stock abundance analysis and environmental assessment Part 1 for 2017 ocean salmon fishery regulations Pacific Fishery Management Council (Salmon Technical Team) Pacific Fishery Management Council, Portland, Oregon. 131 p.

Preseason report II: Proposed alternatives and environmental assessment Part 2 for 2017 ocean salmon fishery regulations Pacific Fishery Management Council (Salmon Technical Team) Pacific Fishery Management Council, Portland, Oregon. 67 p.

Preseason report III: Council adopted management measures and environmental assessment Part 3 for 2017 ocean salmon fishery regulations Pacific Fishery Management Council (Salmon Technical Team) Pacific Fishery Management Council, Portland, Oregon. 48 p.

Combining functional data with hierarchical Gaussian process models Poynor, Valerie, and Stephan Munch Environmental and Ecological Statistics 24(2):175-199

Pacific sardine STAR Panel meeting report (NOAA / Southwest Fisheries Science Center, La Jolla, California, February 21-23, 2017) Punt, Andre, Will Satterthwaite, Evelyn Brown, Jon Volstad, and Gary Melvin In: April 2017 Briefing Book, Agenda item G.5.a, STAR Panel report (24 p.). Pacific Fishery Management Council, Portland, Oregon.

Genetic assignment with isotopes and habitat suitability (GAIAH), a migratory bird case study Ruegg, Kristen C., Eric C. Anderson, Ryan J. Harrigan, Kristina L. Paxton, Jeffrey F. Kelly, Frank Moore, and Thomas B. Smith Methods in Ecology and Evolution 8(10):1241-1252

Central Valley passive integrated transponder (PIT) tag array feasibility study Rundio, David E., Alina N. Montgomery, Matthew G. Nesbit, Matthew S. Morris, Gabriel T. Brooks, Gordon A. Axel, Jesse J. Lamb, Richard W. Zabel, John Ferguson, and Steven T. Lindley U.S. Department of Commerce, NOAA Technical Memorandum NMFS-SWFSC-573. 118 p.

A framework for informing permitting decisions on scientific activities in marine protected areas Saarman, Emily T., Brian Owens, Richard F. Ambrose, Mark H. Carr, John C. Field, Steven N. Murray, Karina J. Nielsen, and Stephen B. Weisberg Report to the California Department of Fish and Wildlife. California Ocean Protection Council, Science Advisory Team. 61 p.

Effective population sizes of a major vector of human diseases, Aedes aegypti Saarman, Norah P., Andrea Gloria-Soria, Eric C. Anderson, Benjamin R. Evans, Evlyn Pless, Luciano V. Cosme, Cassandra Gonzalez-Acosta, Basile Kamgang, Dawn M. Wesson, and Jeffrey R. Powell Evolutionary Applications 10(10):1031-1039

Cruise report, NOAA Ship Reuben Lasker RL-17-03, April 26 - June 13, 2017: Rockfish recruitment and ecosystem assessment Sakuma, Keith NOAA National Marine Fisheries Service, SWFSC Fisheries Ecology Division, Santa Cruz, California. 20 p.

Impacts of ocean climate variability on biodiversity of pelagic forage species in an upwelling ecosystem Santora, Jarrod A., Elliott L. Hazen, Isaac D. Schroeder, Steven J. Bograd, Keith M. Sakuma, and John C. Field Marine Ecology Progress Series 580:205-220

Persistence of trophic hotspots and relation to human impacts within an upwelling marine ecosystem Santora, Jarrod A., William J. Sydeman, Isaac D. Schroeder, John C. Field, Rebecca R. Miller, and Brian K. Wells Ecological Applications 27(2):560-574

Ocean size and corresponding life history diversity among the four run timings of California Central Valley Chinook Salmon Satterthwaite, William H., Stephanie M. Carlson, and Anne Criss Transactions of the American Fisheries Society 146(4):594-610

Projecting marine mammal distribution in a changing climate Silber, Gregory K., Matthew D. Lettrich, Peter O. Thomas, Jason D. Baker, Mark Baumgartner, Elizabeth A. Becker, Peter Boveng, Dorothy M. Dick, Jerome Fiechter, Jaume Forcada, Karin A. Forney, Roger B. Griffis, Jonathan A. Hare, Alistair J. Hobday, Daniel Howell, Kristin L. Laidre, Nate Mantua, Lori Quakenbush, Jarrod A. Santora, Kathleen M. Stafford, Paul Spencer, Charles Stock, William Sydeman, Kyle Van Houtan, and Robin S. Waples Frontiers in Marine Science 4:413 (14 p.)

Patterns of movement, growth, and survival of adult sablefish (Anoplopoma fimbria) at contrasting depths in slope waters off Oregon Sogard, Susan M., and Steven A. Berkeley Fishery Bulletin 115(2):233-251

Abundance estimates and confidence intervals for the run composition of returning salmonids Steinhorst, Kirk, Timothy Copeland, Michael W. Ackerman, William C. Schrader, and Eric C. Anderson Fishery Bulletin 115(1):1-12

Estimating partial regulation in spatiotemporal models of community dynamics Thorson, James T., Stephan B. Munch, and Douglas P. Swain Ecology 98(5):1277-1289

Predicting life history parameters for all fishes worldwide Thorson, James T., Stephan B. Munch, Jason M. Cope, and Jin Gao Ecological Applications 27(8):2262-2276

Genetic and life-history consequences of extreme climate events Vincenzi, Simone, Marc Mangel, Dusan Jesensek, John Carlos Garza, and Alain J. Crivelli Proceedings of the Royal Society B 284(1848):20162118 (8 p.)

Using choice models to inform large marine protected area design Wallmo, Kristy, and Rosemary Kosaka Marine Policy 83:111-117

Purging putative siblings from population genetic data sets: a cautionary view Waples, Robin S., and Eric C. Anderson Molecular Ecology 26(5):1211-1224

State of the California Current 2016-17: Still anything but "normal" in the north Wells, Brian K., Isaac D. Schroeder, Steven J. Bograd, Elliott L. Hazen, Michael G. Jacox, Andrew Leising, Nathan Mantua, Jarrod A. Santora, Jennifer Fisher, William T. Peterson, Eric Bjorkstedt, Roxanne R. Robertson, Francisco P. Chavez, Ralf Goericke, Raphael Kudela, Clarissa Anderson, Bertha E. Lavaniegos, Jose Gomez-Valdes, Richard D. Brodeur, Elizabeth A. Daly, Cheryl A. Morgan, Toby D. Auth, John C. Field, Keith Sakuma, Sam McClatchie, Andrew R. Thompson, Edward D. Weber, William Watson, Robert M. Suryan, Julia Parrish, Jane Dolliver, Stephanie Loredo, Jessica M. Porquez, Jeannette E. Zamon, Stephanie R. Schneider, Richard T. Golightly, Pete Warzybok, Russell Bradley, Jaime Jahncke, William Sydeman, Sharon R. Melin, John A. Hildebrand, Amanda J. Debich, and Bruce Thayre CalCOFI Reports 58:1-55

Environmental conditions and prey-switching by a seabird predator impact juvenile salmon survival Wells, Brian K., Jarrod A. Santora, Mark J. Henderson, Pete Warzybok, Jaime Jahncke, Russell W. Bradley, David D. Huff, Isaac D. Schroeder, Peter Nelson, John C. Field, and David G. Ainley Journal of Marine Systems 174:54-63

Scientific framework for assessing factors influencing endangered Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha) across the life cycle Windell, Sean, Patricia L. Brandes, J. Louise Conrad, John W. Ferguson, Pascale A.L. Goertler, Brett N. Harvey, Joseph Heublein, Joshua A. Israel, Daniel W. Kratville, Joseph E. Kirsch, Russell W. Perry, Joseph Pisciotto, William R. Poytress, Kevin Reece, Brycen G. Swart, and Rachel C. Johnson U.S. Department of Commerce, NOAA Technical Memorandum NMFS-SWFSC-586. 49 p.

parallelnewhybrid: an R package for the parallelization of hybrid detection using NewHybrids Wringe, Brendan F., Ryan R.E. Stanley, Nicholas W. Jeffery, Eric C. Anderson, and Ian R. Bradbury Molecular Ecology Resources 17(1):91-95

hybriddetective: A workflow and package to facilitate the detection of hybridization using genomic data in R Wringe, Brendan F., Ryan R.E. Stanley, Nicholas W. Jeffery, Eric C. Anderson, and Ian R. Bradbury Molecular Ecology Resources 17(6):e275-e284

Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens) Zhen, Ying, Ryan J. Harrigan, Kristen C. Ruegg, Eric C. Anderson, Thomas C. Ng, Sirena Lao, Kirk E. Lohmueller, and Thomas B. Smith Molecular Ecology 26(19):4966-4977

Population genetic structure and ancestry of steelhead/rainbow trout (Oncorhynchus mykiss) at the extreme southern edge of their range in North America Abadia-Cardoso, Alicia, Devon E. Pearse, Sandra Jacobson, Jack Marshall, Dale Dalrymple, Frank Kawasaki, Gorgonio Ruiz-Campos, and John Carlos Garza Conservation Genetics 17(3):675-689

Historia evolutiva y biodiversidad genetica de las truchas de la Sierra Madre Occidental Abadia-Cardoso, Alicia, Francisco Javier Garcia-De Leon, and John Carlos Garza In: Arturo Ruiz-Luna and Francisco Javier Garcia-De Leon (eds), La trucha dorada Mexicana, p. 29-38. Centro de Investigacion en Alimentacion y Desarrollo (CIAD); Consejo Nacional de Ciencia y Tecnologia (CONACYT); Centro de Investigaciones Biologicas del Noroeste (CIB).

Primerias gestiones para el cultivo de trucha nativa de la Sierra Madre Occidental: recolecta, determinacion de identidad genetica y reproduccion Abadia-Cardoso, Alicia, Jose Luis Damas-Aguilar, Jose Luis Falcon-Rodriguez, Francisco Javier Garcia-De Leon, John Carlos Garza, and Genoveva Ingle de la Mora In: Arturo Ruiz-Luna and Francisco Javier Garcia-De Leon (eds), La trucha dorada Mexicana, p. 153-171. Centro de Investigacion en Alimentacion y Desarrollo (CIAD); Consejo Nacional de Ciencia y Tecnologia (CONACYT); Centro de Investigaciones Biologicas del Noroeste (CIB).

Bayesian pedigree inference with small numbers of single nucleotide polymorphisms via a factor-graph representation Anderson, Eric C., and Thomas C. Ng Theoretical Population Biology 107:39-51

Parallel evolution of the summer steelhead ecotype in multiple populations from Oregon and Northern California Arciniega, Martha, Anthony J. Clemento, Michael R. Miller, Matt Peterson, John Carlos Garza, and Devon E. Pearse Conservation Genetics 17(1):165-175

Marine fisheries Bjorkstedt, Eric P., John C. Field, Milton Love, Laura Rogers-Bennett, and Rick Starr In: Harold Mooney and Erika Zavaleta (eds.), Ecosystems of California, p. 779-815. University of California Press.

South-Central/Southern California Coast Recovery Domain Boughton, David A. In: Thomas H. Williams et al. (eds.), Viability assessment for Pacific salmon and steelhead listed under the Endangered Species Act: Southwest, p. 109-128. U.S. Department of Commerce, NOAA Technical Memorandum NMFS-SWFSC-564.

Removing a dam and re-routing a river: Will expected benefits for steelhead be realized in Carmel River, California? Boughton, David A., Amy East, Larry Hampson, Joseph D. Kiernan, Sheldon Leiker, Nathan Mantua, Colin Nicol, Douglas Smith, Kevan Urquhart, Thomas H. Williams, and Lee R. Harrison U.S. Department of Commerce, NOAA Technical Memorandum NMFS-SWFSC-553. 85 p.

Close-kin mark-recapture Bravington, Mark V., Hans J. Skaug, and Eric C. Anderson Statistical Science 31(2):259-274

Climate science strategy of the US National Marine Fisheries Service Busch, D. Shallin, Roger Griffis, Jason Link, Karen Abrams, Jason Baker, Russell E. Brainard, Michael Ford, Jonathan A. Hare, Amber Himes-Cornell, Anne Hollowed, Nathan J. Mantua, Sam McClatchie, Michelle McClure, Mark W. Nelson, Kenric Osgood, Jay O. Peterson, Michael Rust, Vincent Saba, Michael F. Sigler, Seth Sykora-Bodie, Christopher Toole, Eric Thunberg, Robin S. Waples, and Richard Merrick Marine Policy 74:58-67

Why do larger mothers produce larger offspring? A test of classic theory Cameron, Hayley, Keyne Monro, Martino Malerba, Stephan Munch, and Dustin Marshall Ecology 97(12):3452-3459

Ecosystem models for fisheries management: finding the sweet spot Collie, Jeremy S., Louis W. Botsford, Alan Hastings, Isaac C. Kaplan, John L. Largier, Patricia A. Livingston, Eva Plaganyi, Kenneth A. Rose, Brian K. Wells, and Francisco E. Werner Fish and Fisheries 17(1):101-125.

Assessments of California, Oregon and Washington stocks of black rockfish (Sebastes melanops) in 2015 Cope, Jason M., David Sampson, Andi Stephens, Meisha Key, Patrick P. Mirick, Megan Stachura, Tien-Shui Tsou, Phillip Weyland, Aaron Berger, Troy Buell, Elizabeth Councill, E.J. Dick, Kari H. Fenske, Melissa Monk, and Brett T. Rodomsky Pacific Fishery Management Council, Portland, Oregon. 402 p.

Climate and ocean conditions Crozier, Lisa G., and Nathan J. Mantua In: Thomas H. Williams et al. (eds.), Viability assessment for Pacific salmon and steelhead listed under the Endangered Species Act: Southwest, p. 8-17. U.S. Department of Commerce, NOAA Technical Memorandum NMFS-SWFSC-564.

Use of age- and stage-structured matrix models to predict life history schedules for semelparous populations Davison, Raziel J., and William H. Satterthwaite Natural Resource Modeling 29(4):538-558