THE UNIVERSITY OF SOUTH FLORIDA
UNIVERSITY OF SOUTH FLORIDA -- COLLEGE OF MARINE SCIENCE
SPRING SEMESTER 2005
Syllabus
EVOLUTION AND ECOLOGY OF REEFS
12886 OCG 6668 (614) - 3 credits
Tuesdays 5-8 pm Location: MSL Conference Room
Instructor: Dr. Pamela Hallock Muller Office: MSL 203 Phone: 727-553-1567
e-mail: pmuller@marine.usf.edu Office hours: by appointment
Date Topic Reading Assignment Disc. Leaders
Jan. 11 Introduction to course & to coral reefs Veron (2000) PHM
Jan. 18 Physical Controls on Reef Growth Hubbard (in press) PHM
Veron (1995): Chap. 6
Jan. 25 Coral –Algal Symbiosis/Coral Reproduction Muller-Parker & D’Elia (1997) PHM Baker (2003)
Richmond (1997)
Feb. 1 Calcification Cohen & McConnaughey (2003) class
Gattuso et al. (1999) PHM
Feb. 8 Algae, nutrient cycles, and Dawes (1998) 1.
primary production on the reef Jompal & McCook (2003) 2.
Dubinsky and Berman-Frank (2001) 3.
Feb. 15 Bleaching and disease Douglas (2003) 1.
Coles & Brown (2003) 2.
Sutherland et al. (2004) 3.
Feb. 22 Coral reef invertebrates: taxonomy, Carpenter (1997) 1.
ecologic and geologic roles Pennings (1997) 2.
Glynn (in press) 3.
Mar. 1 Coral Reef Monitoring and Restoration Jaap (2000) WCJ Walter Jaap, FMRI Jaap & McField (2001) WCJ
Mar. 8 Reef Fish: taxonomy, ecology, To be announced 1.
management Hixon (1997) 2.
McManus et al. (2000) 3.
Mar. 15 Spring Break
Mar. 22 Diversity and biogeography of reefs Veron (2000)/Fukami et al (2004) 1.
Birkeland (1997) 2.
Pauley (1997) 3.
Mar. 29 Role of disturbance on coral reefs Koop et al. (2001) 1.
Hughes & Connell (1999) 2.
McManus & Polsenberg (2004) 3.
Apr. 5 Pleistocene History of Reefs Quinn & Sampson (2002) 1.
Pandolfi (2002) 2.
Blanchon and Shaw (1995) 3.
Apr. 12 Coral reefs and global change Pandolfi et al. (2003) 1.
Guinotte et al. (2003) 2.
Hoegh-Guldberg (2004) 3.
Apr. 19 Reef management and preservation Hughes et al. (2003) 1.
Birkeland (1997) 2.
Hempel & Morozova (2001) 3.
Apr. 26 Student Presentations
May 3 Student Presentations
Course Objectives: Coral reefs worldwide are threatened by human activities ranging from local boat groundings to global change processes. The objectives of this course are to examine issues critical to coral-reef growth and preservation. Topics include what coral reefs are, how they are formed, the kinds of organisms that make up the reef community, environmental qualities required for reefs to thrive, the importance of coral reefs to mankind, how human activities are affecting coral reefs, and an introduction to reef management.
Grading Policy: See page 6 for specific details for each assignment
Class participation (@ 12 classes x 5 points/class) 60 points (24%)
Discussion leader (@4 x 20 points/presentation) 80 points (32%)
Abstract (Due February 15) 10 points (4%)
Manuscript (Due Apr. 26; late deduction 1 pt/day) 60 points (24%)
Oral Presentation (Apr. 26 or May 3) 40 points (16%)
Discussion Leaders: Most weeks, 2 or 3 students will be assigned as discussion leaders. Each student leader will be responsible for presenting and leading discussion on one of the assigned readings. Recommended format is to spend 15-20 minutes summarizing key points of the reading, using overheads or computer/ LCD projector. Scoring for discussion leaders will be based on an average of the score assigned by the instructor and class members, deleting the highest and lowest student scores.
Class Participation: The success of the course to enrollees depends on active and enthusiastic preparation for and participation in each class. Each student should bring at least one discussion question for each reading assignment, for discussion by the class after the summary. Weekly scores will be based upon participation level: 5 point score for active and voluntary participation in discussion; 4 point score for thoughtful discussion when called upon; 3 points for attendance with minimal participation in the discussion.
Attendance Policy: Since 24% of the course grade will be based on weekly participation in discussion of the readings, class attendance is required. Recognizing research and meeting commitments, students can miss up to two classes without makeup. If you must miss more than two classes, your make-up assignment is to write a one-page synthesis of each reading assigned for that class.
Please note that students who anticipate being absent from class due to religious observance should inform the instructor by the second class meeting.
Project: The last two class meetings will serve as a mini-symposium for student projects. Each students will a) prepare a 300-word abstract on a proposed topic (due February 15),
b) write a short paper (15 pages double spaced maximum) on that topic (due April 26),
c) make a meeting-style 15-20 minute presentation (Apr. 26 or May 3),
Advanced students are encouraged to present an aspect of their thesis or dissertation research, using this venue to prepare a piece of their work for a scientific meeting and submission of a paper for publication. Beginning and special students may select to write a literature review for their possible thesis or dissertation topic. See for a useful reference on writing literature reviews. Science educators may choose to develop a teaching exercise that presents some aspect of reef biology or geology. When you get an idea for a project, discuss it with Dr. Muller in person or by e-mail. Grading of abstracts, presentations and papers is explained on page 6. Oral presentations will be scored by both instructor and class members, final score will be based on an average of the score assigned by the instructor and class members, deleting the highest and lowest student scores.
Assigned readings not available in PDF format will be available in a binder labeled “Evolution and Ecology of Reefs” in MSL 2nd Floor Reading area. (**PDF can be downloaded through USF Virtual Library; ***manuscript can be printed through USF Virtual Library)
Jan. 11. Introduction
Veron, J.E.N. 2000. Corals of the World, Vol. 1. Australian Institute of Marine Science, p. 21-29; 47-56.
Veron, J.E.N. 2000. Corals of the World, Vol. 3. Australian Institute of Marine Science, p. 425-433.
Jan. 18. Physical Controls
Hubbard, D.K. Reefs as dynamic systems. In Birkeland, C. (ed), Life and Death of Coral Reefs 2nd Edition, Chapman and Hall, New York. (in press – PDF available)
Veron, J.E.N. 1995. Chapter 6. The physical environment. Corals in Space and Time, The Biogeography and Evolution of the Scleractinia. Comstock/Cornell, Ithaca and London, p. 89-104.
Jan. 25. Coral –Algal Symbiosis/Coral Reproduction
Muller-Parker, G. and D’Elia, C.F. 1997. Interactions between corals and their symbiotic algae. In Birkeland, C. (ed), Life and Death of Coral Reefs, Chapman and Hall, New York, p. 96-113.
Baker, A.C. 2003. Flexibility and specificity in coral-algal symbiosis: Diversity, ecology and biogeography of Symbiodinium. Annual Reviews of Ecology, Evolution and Systematics 34:661-689.***
Richmond, R.H. 1997. Reproduction and recruitment in corals: Critical links in the persistence of coral reefs. In Birkeland, C. (ed), Life and Death of Coral Reefs, Chapman and Hall, New York, p. 175-197.
Feb. 1. Calcification
Cohen, A.L. and McConnaughey, T.A. 2003.Geochemical perspectives on coral biomineralization. Reviews in Mineralogy and Geochemistry 54: 151-187. [PDF available at ]
Gattuso, J.P., Allemand, D., and Frankignoulle, M. 1999. Photosynthesis and calcification at cellular, organismal and community levels in coral reefs: A review on interactions and control by carbonate chemistry. American Zoologist 39:160-183. ***[]
Feb. 8. Algae, nutrient cycles, and primary production
Dawes, C.J. 1998. Marine plants of coral reefs. In Dawes, C.J. Marine Botany, 2nd edition. Wiley, New York, p. 346-367 (note: pages 338-346 are general information).
Jompal, J. and McCook, L.J. 2003. Coral–algal competition: macroalgae with different properties have different effects on corals. Marine Ecology – Progress Series 258:87-96.**
Dubinsky, Z., and Berman-Frank, I. 2001. Uncoupling primary production from population growth in photosynthesizing organisms in aquatic ecosystems. Aquatic Sciences 63:4-17.**
Feb. 15. Bleaching and Disease
Douglas, A.E. 2003. Coral bleaching - how and why? Marine Pollution Bulletin 46 (4): 385-392.**
Coles, S.L. and Brown, B.E. 2003. Coral bleaching - Capacity for acclimatization and adaptation. Advances in Marine Biology 46: 183-223. []
Sutherland, K.P., J.W. Porter, and C. Torres. 2004. Disease and immunity in Caribbean and Indo-Pacific zooxanthellate corals. Marine Ecology-Progress Series, 266: 273-302.**
Feb. 22. Coral-reef invertebrates
Carpenter, R.C. 1997. Invertebrate predators and grazers. In Birkeland, C. (ed), Life and Death of Coral Reefs, Chapman and Hall, New York, p. 198-229.
Pennings, S.C. Indirect interactions on coral reefs. In Birkeland, C. (ed), Life and Death of Coral Reefs, Chapman and Hall, New York, p. 249-272.
Glynn, P.W. Bioerosion and coral-reef growth: A dynamic balance. In Birkeland, C. (ed), Life and Death of Coral Reefs 2nd edition, Chapman and Hall, New York (in press – PDF available).
Mar. 1. Coral reef monitoring and restoration
Jaap, W.C., and McField, M.D. 2001. Video sampling for monitoring coral-reef benthos. Bulletin of the Biological Society of Washington 10:269-273.
Jaap, W.C. 2000. Coral reef restoration. Ecological Engineering 15:345-364.**
Mar. 8. Coral-reef fish:
To be announced
Hixon, M.A. 1997. Effects of reef fishes on corals and algae. In Birkeland, C. (ed), Life and Death of Coral Reefs, Chapman and Hall, New York, p. 230-248.
McManus, J.W., Menez, L.A.B., Kesner-Reyes, K.N., Vergara, S.G., and Ablan, M.C. 2000. Coral reef fishing and coral-algal phase shifts: implications for global reef status. ICES Journal of Marine Science 57:572-578.**
Mar. 22. Diversity and biogeography
Veron, J.E.N. 2000. Corals of the World, Vol. 3. Australian Institute of Marine Science, p. 411-421.
Fukami, H., Budd, A.F., Paulay, G., Sole-Cava, A., Chen, C.L.A., Iwao, K., Knowlton, N. 2004. Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals. Nature 427 (6977): 832-835.***
Birkeland, C. 1997. Geographic differences in ecological processes on coral reefs. In Birkeland, C. (ed), Life and Death of Coral Reefs, Chapman and Hall, New York, p.273-287.
Paulay, G. 1997. Diversity and distribution of reef organisms. In Birkeland, C. (ed), Life and Death of Coral Reefs, Chapman and Hall, New York, p. 298-253.
Mar. 29. Role of disturbance
Hughes, T.P., and Connell, J.H. 1999. Multiple stressors on coral reefs: A long-term perspective. Limnology and Oceanography 44 (3, Part 2): 932-940.**
Koop, K., Booth, D., Broadbent, A., Brodie, J., Bucher, D., Capone, D., Coll, J., Dennison, W., Erdmann, M., Harrison, P., Hoegh-Guldberg, O., Hutchings, P., Jones, G.B., Larkum, A.W.D., O'Neil, J., Steven, A., Tentori, E., Ward, S., Williamson, J., and Yellowlees, D. 2001. ENCORE: The effect of nutrient enrichment on coral reefs. Synthesis of results and conclusions. Marine Pollution Bulletin 42:91-120.**
McManus, J.W. and Polsenberg, J.F. 2004. Coral-algal phase shifts on coral reefs: ecological and environmental aspects. Progress in Oceanography 60 (2-4): 263-279.**
Apr. 5. Pleistocene history of reefs
Quinn, T.M. and Sampson, D.E. 2002. A multiproxy approach to reconstructing sea surface conditions using coral skeleton geochemistry. Paleoceanography 17 (4): Art. No. 1062.
Pandolfi, J.M. (2002) Community Dynamics at multiple scales. Coral Reefs 21:13-23.**
Blanchon, P. and Shaw, J. 1995. Reef drowning during the last glaciation: Evidence for catastrophic sea-level rise and ice sheet collapse. Geology 23:4-8.
Apr. 12
Pandolfi, J.M., Bradbury, R.H., Sala, E., Hughes, T.P., Bjorndal, K.A., Cooke, R.G., McArdle, D., McClenachan, L., Newman, M.J.H., Paredes, G., Warner, R.R., Jackson, J.B.C. 2003. Global trajectories of the long-term decline of coral reef ecosystems. Science 301 (5635): 955-958.**
Guinotte, J.M., Buddemeier, R.W., and Kleypas, J.A. 2003. Future coral reef habitat marginality: temporal and spatial effects of climate change in the Pacific basin. Coral Reefs 22 (4): 551-558.**
Hoegh-Guldberg, O. 2004. Coral reefs in a century of rapid environmental change. Symbiosis 37 (1-3): 1-31.
Apr. 13
Birkeland, C. Implications for resource management. In Birkeland, C. (ed), Life and Death of Coral Reefs, Chapman and Hall, New York, p. 411-435.
Hughes, T.P., Baird, A.H., Bellwood, D.R., Card, M., Connolly, S.R., Folke, C., Grosberg, R., Hoegh-Guldberg, O., Jackson, J.B.C., Kleypas, J., Lough, J.M., Marshall, P., Nystrom, M., Palumbi, S.R., Pandolfi, J.M., Rosen, B., and Roughgarden, J. 2003. Climate change, human impacts, and the resilience of coral reefs. Science 301 (5635): 929-933.***
Hempel, L.C., and Morozova, S. 2001. Science into policy: Designing coral reef management from the benthos up. Bulletin of Marine Science 69:945-966.***
GRADING OF ASSIGNMENTS
Reading Assignment Discussion Leader: _______________________________
Understanding of assignment (10 points) __________
Oral presentation (5 points) __________
(communication of key points of assignment)
Creativity in leading discussion (5 points) __________
(quality of visual aids and/or approach)
Total (20 points/assignment led) __________
Abstract: _______________________________
Succinct, descriptive title (2 points) __________
Statement of purpose (2 points) __________
Methods sentence(s) (1 points) __________
Anticipated Results (1 points) __________
Significance (2 points) __________
Writing style (2 points) __________
Total (10 points possible) __________
Project Presentation: _______________________________
Scientific content (30 points possible) __________
Oral presentation (5 points possible) __________
Creativity (5 points possible) __________
(quality of visual aids and/or approach)
Total (40 possible) __________
Final Paper:
Scientific content (45 points possible) __________
Organization, readability (5 points possible) __________
Citations and referencing (5 points possible) __________
Grammar, spelling (5 points possible) __________
Total (60 possible) __________
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