Syllabus

Winter 1999

Fish 497U, Winter 1999, 2 Credits

The Puget Sound Basin and Salmon:
Developing a Scientific Basis of Understanding

Good thinking proceeds from the friction between reflective thought and real problems.


Time and Place

Wednesday Evening, 7-9 PM; Room 201 Fisheries Center

Course Coordinator

Robert C. Francis, 454 Fisheries Center, 543-7345, e-mail: rfrancis@fish.washington.edu
Office Hours: Wed 5:30 - 6:30 PM, Room 207 Fisheries Center

Teaching Assistant

Julie Nelson, email: jnels@u.washington.edu

Course Objectives and Format

The intent of the course is to provide a scientific context for developing an understanding of the issue of salmon in Puget Sound - ranging from the physical structure of the Puget Sound Basin, Basin hydrology and oceanography, Puget Sound salmonid life histories, habitat needs and production histories, salmonid ESA listing criteria, Puget Sound salmon stock assessments and ESA recommendations, and past institutional responses to salmonid ESA listings.

The course is offered each Wednesday evening (7-9 PM, Room 201 Fisheries Center) during Winter Quarter 1999 as a 400 level undergraduate graded course in the College of Ocean and Fishery Sciences (Fish 497U) as well as by UW Extension for the greater Puget Sound community. Students taking the course for credit will do term projects on various aspects of the issue of interest to them, and will make both written and oral presentations of their results.

The course is sponsored by the PRISM (Puget Sound Regional Synthesis Model) UIF project under the guidance of the PRISM Education Committee. The mission of PRISM is to develop and sustain a dynamic and integrated understanding and description of the environmental and human factors that shape the Puget Sound Region.

Week 1 (Jan 6) A Puget Sound and Salmon Primer - Bob Francis

      The Lay of the Land- Ralph Haugerud
      Overview of Species, life histories, ecology, habitat needs, 
				  genetics - Tom Quinn
							

Week 2 (Jan 13) Introduction to the Physical/Biological Structure 
and Dynamics of Puget Sound Biological Production- R Strickland, J Newton

      Circulation Physical Forcing, Climate- Glenn Cannon
      Biological production I (primary, secondary - food chain) - J Newton


Week 3 (Jan 20) Puget Sound Biophysical Connections to Salmon - Newton 
and Strickland

      Estuarine, Nearshore - Si Simenstad
      Contaminants and Pollution - Alan Mearns
      Predators - Steve Jeffries


Week 4 (Jan 27) Connections to the Land - Melvin

      Freshwater Hydrology- Tim Beechie
      Terrestrial Habitat Influences- Bob Bilby


Week 5 (Feb 3) Humans and the Salmon Resources of the Puget Sound - Francis
and Melvin

      Harvest - Ray Hilborn
      Hatcheries and Aquaculture- Bill Hershberger
      Putting the physics and biology together- Bill Pinnix


Week 6 (10 Feb) The ESA and its Scientific Basis - Maxson

      Robin Waples NOAA/ NMFS
      Bill Tweit WDFW


Week 7 (17 Feb) What's Being Done: Salmon Restoration, Habitat Protection
      and Citizen Activism: Panel Discussion - Maxson and Copping	
				
      Gino Lucchetti- Metro, King County
      Al Latham- Olympic Penninsula
      Lynn Best- Seattle City Light
      Mike Grayum- NW Indian Fisheries Commission

Week 8 (24 Feb) Turning things Around- Can it be done?: Panel Discussion- Copping

      Bob Fuerstenberg- Metro, King County
      Dave Fluharty- School of Marine Affairs, UW
      Derek Booth- ?
      Tim Douglas- Community Trade and Economic Development


Week 9 (3 Mar) Student Posters

Week 10 (10 Mar) What Have We Learned? Open Panel discussion with all speakers and 
students

Weekly Class Format:

The general format of the course is to invite 2 or 3 speakers into class each week to make presentation with the last 2 weeks of lecture being panel discussions. Each speaker will specify one required reading and several optional readings. All required readings will be on reserve in the Fisheries/Oceanography Library and Odegaard Undergraduate Library. In addition, the required readings will be available electronically from the UW libraries web page. Optional or recommended readings will be listed on the course web page.

Library Web Page (http://www.lib.washington.edu/)

Our TA, Julie Nelson, is developing a course web page which should be quite a resource for the students as well as the general PRISM community. Each of the 10 sessions will be outlined as a separate entity on the web. At a minimum we want to include a lecture outline and a list of readings for each speaker. The web page will also have an interactive section. Questions can be posed and we will attempt to answer them as quickly as possible.

Course Web Page (http://courses.washington.edu/fish497u/)

Grading Policy:

Grades (CR,NC) will be based on three assignments. Student registered for credit will divide into groups of (aprox.) 5 and:

Three Assignments:

1. Each student will develop a poster presentation on some issue relating to the Puget Sound Basin and salmon. All posters will be displayed during class on week 9. The UW Office of Community Service and Education has already contacted 3 salmon groups (Thornton Creek Alliance, Save Our Wild Salmon, Piper Creek Alliance) who are willing to each work with a group of students on a term project. One of the major aspects of PRISM is to develop computer-based visualizations of complex processes operating in the Sound. We are hoping that a number of projects might involve working with the PRISM folks to either further develop their visualizations or to develop some new Puget Sound salmon visualizations which might help provide a deeper insight into some aspect of the issue we are dealing with. There are infinite possibilities for projects. We suggest that you sound (no pun intended) ideas out with Prof. Francis and Ms. Nelson during the first several weeks of the quarter so that you can get started on your project early.

2. Write a 5 page (double spaced, max) description of the project and its results.

3. Give a brief (3 min) oral presentation of the project to the class during week 9.

Required Readings:

Required readings available at Fisheries and Ocean Library, Odegaard Undergraduate Library, and on UW libraries web page- http://www.lib.washington.edu

Week 1:

Booth. D.B. and Goldstein, B., 1994, Patterns and Processes of Landscape development by the Puget lobe ice sheet: Washington Division of Geology and Earth Resources, Bulletin 80, p. 207-218

Thorson, R.M. 1989, Glacio-isostatic response of the Puget Sound area, Washington: Geological Society of America Bulletin, v. 101. n.9, p. 1163-1174.

Chapter 2 from Upstream: Salmon and Society in the Pacific Northwest , National Research Council, National Academy of Sciences, National Academy Press, Washington DC, 1996.

Bjornn, T.C. and Reiser, D.W. American Fisheries Society Special Publication 19:83-138, 1991. Habitat Requirements of Salmonids in Streams. Taken from, Influences of Forest and Rangeland Management on Salmonid Fishes and Their Habitats, ed. W.R. Meechan., 1991.

Week 2:

Cannon, G.A., D.E. Bretschneider, and J.R. Holbrook (1984). Transport variability in a fjord, in The Estuary as a Filter, V.S. Kennedy (ed.), Academic Press, pp. 67-78.

Chapters 5&6 from The Fertile Fjord: Plankton in the Puget Sound, Richard Strickland, Puget Sound Books series, Washington Sea Grant Publication,

Week 3:

Lefkovitz, L.F., V.I. Cullinan and E.A. Crecilius. 1997. Historical
trends in the accumulation of chemicals in Puget Sound. NOAA Technical
Memorandum NOS ORCA 111, Silver Spring, MD.

Puget Sound Water Quality Action Team
http://www.wa.gov/puget_sound/

Read the 1998 Puget Sound Update and "How Healthy is Puget Sound". Also,
scan the Action teams "Library" which cites numerous reports submitted of
the past decade.

Simenstad, C. A., K. L. Fresh, and E. O. Salo. 1982. The role of Puget Sound and Washington coastal estuaries in the life history of Pacific salmon: An unappreciated function. Pp. 343-364 in V. S. Kennedy (ed.), Estuarine Comparisons. Academic Press, New York. 709 pp.

Impacts of California sea Lions and Pacific Harbor Seals on Salmonids and on the Coastal Ecosystems of Washington, Oregon and California. NOAA Technical Memorandum NMFS NWFSC- 28, March 1997.

Seattle Times. 1998.Voyage of Discovery: An investigation of Puget Sound, along the route of Capt. George Vancouver.

Week 4:

Bisson, P.A., G. Reeves, R. Bilby and R. Naiman. 1997. Watershed management and Pacific salmon: Desired future conditions. pp. 447-474 in D. Stouder, P. Bisson and R. Naiman (eds.) Pacific salmon and their ecosystems. Chapman and Hall, N.Y.

Benda, L., T.J. Beechie, R.C. Wissmar, and A. Johnson. 1992. Morphology and evolution of salmonid habitats in a recently deglaciated river basin. Canadian Journal of Fisheries and Aquatic Sciences 49(6):1246-1256. A history of salmonid habitat development in a North Cascades watershed after glaciation (i.e., the last ~15,000 years).

Gregory, S.V. and P.A. Bisson. 1997. Degradation and loss of anadromous salmonid habitat in the Pacific Northwest. Pages 277-314 In D.J. Stouder, P.A. Bisson, and R.J. Naiman, eds. Pacific Salmon and their Ecosystems: Status and Future Options. Chapman and Hall, New York. A summary of land-use alterations to salmon habitats in the Pacific Northwest.

Week 5:

Ebbesmeyer, C. C., C. A. Coomes, G. A. Cannon, and D. E. Bretschneider. 1989. Linkage of ocean and fjord dynamics at decadal period. Geophysical Monograph 55: 399-417.

Gargett, A. E. 1997. The optimal stability 'window': a mechanism underlying decadal fluctuations in North Pacific salmon stocks? Fisheries Oceanography 6: 9.

Strickland, R. M. 1983. The Fertile Fjord. Seattle, Washington, University of Washington Press.
Chapters 5 and 6 (see Week 2 readings)

Nosho, Terry Y. Teh Pacific Coast oyster industry: factors contributing to its longevity and sustainability. World Aquaculture 27 (2) June 1996, pp. 10-12.

Nash, Colin E. Salmon Farming then and now. World Aquaculture 26(2) June 1995. pp. 4-10.

Pinnix, Bill D. Marine survival of Puget Sound Coho salmon: Deciphering the climate signal.

Week 6:

Waples, R. S. 1995. Evolutionarily significant units and the conservation of
biological diversity under the Endangered Species Act. American Fisheries
Society Symposium 17:8-27.

Waples, Robin S. 1999. Dispelling some myths about hatcheries. Fisheries vol. 24, no. 2. pp. 12- 21

Waples W.S.1990. Conservation Genetics of Pacific Salmon. Effective population size and the rate of loss of genetic variability. Journal of Heredity 81: 267-276.

WA DNR report, 1998. Our Changing Nature: Natural resource trends in Washington state.

Week 7:

American Friends Service Committee.Uncommon Controversy: the fishing rights of the Muckleshoot, Puyallup, and Nisqually Indians. UW Press, 1970. ch 5.

American Friends Service Committee. Treaties on Trial. UW Press

Bahls, P. and Bahls J.R. 1996. Chimacum Watershed Coho Salmon Restoration Assessment. excerpt from report.

NW Indian Fisheries News. Fall 1998. Vol. XVIII no. 3.

Treaty Indian Tribes of Western WA. 1999. Annual Report: Comprehensive Tribal Natural Resource Management.

Week 8:

Governor's Salmon Recovery Office. Draft Statewide Strategy to recover salmon: Extinction is not an option. January 1999.vol. 1.

Recommended Readings on Reserve: The following books/ reports are on reserve ast the Fish/ OCN Library

Upstream: Salmon and Society in the Pacific Northwest , National Research Council, National Academy of Sciences, National Academy Press, Washington DC, 1996.

Pacific Salmon and Their Ecosystems: Status and Future Options. eds. Stouder, D.J., Bisson, P.A., Naiman, R.J. Chapmann and Hall, New york, NY. 1997.

Pacific Salmon Life Histories. eds.Groot, C.and Margulis, L. UBC Press, Vancouver BC, 1991.

Holtby, L. B. and J.C. Scrivener. 1989. Observed and simulated effects of climate variability, clear-cut logging, and fishing on the numbers of chum salmon (Oncorhynchus keta) and coho salmon (Oncorhynchus kisutch) returning to Carnation Creek, British COlumbia. Canadian Special Publication of Fisheries and Aquatic Sciences 105: 62-81. This is a really incredible paper, and the rest of the volume has some good stuff too.

1992 Washington State Salmon and Steelhead Inventory, WDFW and Washington Treaty Tribes. Olympia, WA 1993. SASSI reoprts for Puget Sound Salmon North Sound and South Sound volumes also on reserve.

Redings on reserve at Odegaard

Puget Sound Research Proceedings, 1991. vol. 1, 2.

Puget Sound Research Proceedings, 1995. vol. 1, 2.

Additional Recommended Readings: Not on reserve

WEEK 1

Willson, M.F. 1997. Variation in salmonid life histories: patterns and perspectives. U.S. FOrest Service Research Paper PNW-RP-498. 50 p. A bit obscure but very interesting.

WEEK 2

Puget Sound Water Quality Action Team. 1998. 1998 Puget Sound Update:
Sixth Report of the Puget Sound Ambient Monitoring Program. Puget Sound
Water Quality Action Team. Olympia, Washington.

Newton, J.A. 1995. Observations of El Niqo weather conditions reflected
in the temperatures and salinities of monitoring stations in Puget Sound.
In Puget Sound Research '95 Proceedings, 2: 979-991.

Harrison, PJ, Mackas, DL, Frost, BW, Macdonald, RW and Crecelius, EA.
1994. An Assessment of Nutrients, Plankton and Some Pollutants in the
Water Column of Juan de Fuca Strait, Strait of Georgia and Puget Sound and
their Transboundary Transport.

Mackas, DL and PJ Harrison, 1997. Nitrogenous nutrient sources and sinks
in the Juan de Fuca Strait/Strait of Georgia/Puget Sound estuarine system:
Assessing the potential for eutrophication. Estuarine Coastal and Shelf
Science, 44:1-21.

Newton, J.A., S.L. Albertson, K. Nakata, and C. Clishe. 1998. Washington
State Marine Water Quality in 1996 and 1997. Washington State
Department of Ecology, Environmental Investigations and Laboratory
Services Program, Publication #98-338, Olympia, WA.

WEEK 3

Healey, M. C. 1982. Juvenile Pacific salmon in estuaries: The life support system. Pp. 315-342 in V. S. Kennedy (ed.) Estuarine Comparisons. Academic Press, New York. 709 pp.

Levings, C. D. 1994. Feeding behavior of juvenile salmon and significance of habitat during estuary and early sea phase. Nordic J. Freshwat. Res. 69: 7-16.

Levings, C. D., C. D. McAllister, J. S. Macdonald, T. J. Brown, M. S. Kotyk, and B. A. Kask. 1989. Chinook salmon (Oncorhyunchus tshawytscha) and estuarine habitat: A transfer experiment can help evaluate estuary dependency. Can. Spec. Publ. Fish. Aquat. Sci 105:116-122.

Levy, D. A., and T. G. Northcote. 1982. Juvenile salmon residency in a marsh area of the Fraser River estuary. Can. J. Fish. Aquat. Sci. 39: 270-276.

Simenstad, C. A. 1997. The relationship of estuarine primary and secondary productivity to salmonid production: bottleneck or window of opportunity? Pp. 133-145 in R. Emmett and M. Schiewe (eds.), Proc. Estuarine and Ocean Survival of Northeastern Pacific Salmon, Proc. Workshop March 20-22, 1996, Newport, OR. NOAA Tech. Memo. NMFS-NWFSC-29, Natl. Marine Fish. Serv., NW Fish. Sci. Center, Seattle, WA. 313pp. (extended abstract).

Simenstad, C. A., and R. C. Wissmar. 1985. d13C evidence of the origins and fates of organic carbon in estuarine and nearshore marine food webs. Mar. Ecol.-Prog. Ser. 22:141-152.

Simenstad, C. A., M. Dethier, C. Levings, and D. Hay. 1997. The Land-Margin Interface of Coastal Temperate Rain Forest Ecosystems: Shaping the Nature of Coastal Interactions. Pp. 149-187 (Chap. 7) in P. Schoonmaker, B. von Hagen, and E. Wolf (eds.) The Rain Forests of Home: Profile of a North American Bioregion. Ecotrust/Interain Pacific and Island Press. 480 pp.

Thom, R. M. 1987. The biological importance of Pacific Northwest estuaries. Northwest Environ. J. 3: 21-42.

Thorpe, J. E. 1994. Salmonid fishes and the estuarine environment. Estuaries 17: 76-93.
Wissmar, R. C., and C. A. Simenstad. 1998. Variability of estuarine and riverine ecosystem productivity for supporting Pacific salmon. Pp. 253-301 in G. R. McMurray and R. J. Bailey (eds.), Change in Pacific Northwest Coastal Ecosystems, NOAA Coastal Ocean Prog., Decision Analysis Series No. 11, NOAA Coastal Ocean Office, Silver Spring, MD. 342 pp.

Dexter, R.N., D.E. Anderson, W.A. Quinlan, L.S. Goldstein, R.M.
Strickland, S.P. Pavlou, J.R. Clayton, Jr., R.M. Kocan and M. Landolt.
1981. A Summary of Knowledge of Puget Sound Related to Chemical
Contaminants. NOAA Technical memorandum OMPA-13. National oceanic and
Atmospheric Administration, Boulder, Colorado.435 pp.

Following a five year investigation of Puget Sound, NOAA published this
detailed review in 1981. The review goes into great detail about sources,
fate, transport and effects of contaminants in Puget Sound, known at that
time. Although there are recent reviews (1998 Puget Sound Update), none
go into the detail reported here, almost 20 years ago. For example, there
is no current report that deals with contaminants from a mass input point
of view. Such an update is greatly needed.

WEEK 4

Hydrology
Booth, D.B., and C.R. Jackson. 1997. Urbanization of aquatic systems: degradation thresholds, stormwater detention, and the limits of mitigation. Journal of the American Water Resources Association 33(5):1077-1090.
Harr, F.H., W. C. Harper, J.T. Krygier, and F.S. Hsieh. 1975. Changes in storm hydrographs after road building and clear-cutting in the Oregon Coast Range. Water Resources Research 11(3):436-444.

Sediment
Cederholm, C.J., L.M. Reid, B.G. Edie, and E.O. Salo. 1982. Effects of forest road erosion on salmonid spawning gravel composition and populations of the Clearwater River, Washington. Pages 1-17 In K.A. Hashagen, ed. Habitat disturbance and recovery: proceedings of a symposium. California Trout, Inc., San Francisco.
Sidle, R.C., A.J. Pierce, and C.L. O’Loughlin. 1985. Hillslope stability and land use. Water Resources monograph Series Volume 11. American Geophysical Union, Washington, D. C.

Large woody debris
Murphy, M.L. and K.V. Koski. 1989. Input and depletion of woody debris in Alaska streams and implications for streamside management. North American Journal of Fisheries Management 9:427-436.
Montgomery, D.R., J.M. Buffington, R.D. Smith, K.M. Schmidt, and G. Pess. 1995. Pool spacing in forest channels. Water Resources Research 31(4):1097-1105.

Quantifying physical habitat losses and restoring habitat-forming processes
Beechie, T., E. Beamer, and L. Wasserman. 1994. Estimating coho salmon rearing habitat and smolt production losses in a large river basin, and implications for restoration. North American Journal of Fisheries Management 14:797-811.
Beechie, T., E. Beamer, B. Collins, and L. Benda. 1996. Restoration of habitat-forming processes in Pacific Northwest watersheds: a locally adaptable approach to salmonid habitat restoration. Pages 48-67 In D. L. Peterson and C. V. Klimas, eds. The Role of Restoration in Ecosystem Management. Society for Ecological Restoration, Madison, Wisconsin.

Habitat dynamics
Benda, L. and T. Dunne. 1997a. Stochastic forcing of sediment supply to channel networks from landsliding and debris flow. Water Resources Research 33(12):2865-2880.

Benda, L. and T. Dunne. 1997b. Stochastic forcing of sediment routing and storage in channel networks. Water Resources Research 33(12):2849-2863.

WEEK 5

Waples, R. S. 1994. Genetic considerations in recovery efforts for Pacific
salmon. Conserv. Biol. 8:884-886.

Allendorf, F. W., and R. S. Waples. 1996. Conservation and genetics of
salmonid fishes. Pages 238-280 in: J. C. Avise and J. L. Hamrick, eds.
Conservation genetics: Case histories from nature. Chapman and Hall, New
York.