Syllabus Advanced Topics in Biological Oceanography MBC€¦ · SEA$Semester®:$Marine$Biodiversity$&$Conservation$ $$$$$AdvancedTopics$inBiological$Oceanography:$Biodiversity$A$1$

SEA Semester®: Marine Biodiversity & Conservation

www.sea.edu Advanced Topics in Biological Oceanography: Biodiversity -‐ 1

Advanced Topics in Biological Oceanography: Biodiversity CAS NS 450 (4 credits) Course Catalog Description (max. 40 words): In-‐depth treatment of a single topic in biological oceanography. Extensive review of classical and contemporary literature. Introduction and practice of current laboratory techniques. Oral presentation and written research proposal required. Topics may include marine plankton ecology, marine biodiversity, and satellite oceanography. Instructor(s): Sea Education Association Oceanography Faculty Location: SEA campus in Woods Hole, MA and at sea aboard an SEA sailing school vessel. Prerequisites: Admission to SEA Semester. Three lab science courses (one at the 300-‐level or higher) or consent of instructor. Course Philosophy and Approach: This course is part of the suite of required courses in the SEA Semester: Marine Biodiversity and Conservation (MBC) program. Collectively, the MBC courses provide the context, tools, and opportunity for students to make authentic contributions to the international effort to protect the Sargasso Sea ecosystem. This course builds scientific foundations in marine biodiversity. Global and regional patterns of marine biodiversity are examined through review of classical and contemporary literature. Connections between biodiversity and ecosystem function are explored during interdisciplinary seminar discussion sessions. Laboratory exercises emphasize current methods for sample processing, data collection and assessing marine biodiversity.

Field research is central to the study of marine biodiversity. Throughout the first 5 weeks, students will explore the scientific process as they develop research inquiries, plan sample collection strategies and craft a thorough collaborative research proposal focused on a select group of ecologically and/or economically important organisms (e.g., eel larvae, spiny lobster larvae, the Sargassum-‐associated community, or the microbial community) in the Sargasso Sea ecosystem. Advanced Topics in Biological Oceanography: Biodiversity serves as the precursor to Directed Oceanographic Research.

This course consists of 15 lecture sessions (22 hours combined), 5 laboratory sessions (14 hours combined), a final exam (4 hours), 4 student-‐led Interdisciplinary Seminar discussions (6 hours combined, shared with Ocean Science and Public Policy course), 3 Marine Protection Case Study sessions (12 hours combined, shared with Advanced Ocean Policy Research course), 5 field trips (14 hours combined), and 4 scheduled research project development sessions (7 hours combined).



Learning Outcomes: Students will be able to . . .

1. describe regional oceanography and biodiversity status of the Sargasso Sea region. 2. employ current methods for measuring and assessing marine biodiversity. 3. read, analyze and evaluate scientific literature to determine promising and critical lines

of biodiversity research in the Sargasso Sea region. 4. compose a professional research proposal – following guidelines for Collaborative

Research from the National Science Foundation.

Evaluation: Problem Set 20% Lab Assignments 10% Interdisciplinary Seminar Session (moderator) 5% Interdisciplinary Seminars (participant) 5% Research Group Meeting Assignments 10% Oral Defense of Research Proposal 15% Research Proposal (NSF format) 25% Peer/Self Evaluation of Team Contribution 10% Assignments: Problem Set: A take-‐home, open-‐note problem set will evaluate your understanding of core concepts presented in readings and during lecture and laboratory sessions.

Lab Assignments: To be completed during each laboratory session, these assignments are designed to evaluate application of skills.

Interdisciplinary Seminars: Four Interdisciplinary Seminars will offer opportunities to explore issues central to marine biodiversity and ocean conservation. These discussions should in some ways expand our understanding of important issues—but also model the different perspectives we will need to embrace in developing science, conservation, and communication strategies and policies. Student teams will be assigned as facilitators for each session. Facilitators will coordinate to deliver opening remarks that succinctly summarize key points from the reading and set an agenda, as well as share responsibility for guiding discussion.

Research Group Meeting Assignments: Through a series of research-‐focused seminars, we will work through the steps of research proposal preparation – successful proposal elements, identifying relevant literature, and drafting proposal sections. Thoughtful and well-‐prepared participation during research group meetings is expected of each student.

Oral Defense of Research Proposal: Each student working group will share their research plan in an oral presentation prior to departure for the cruise.

Research Proposal: Each student working group will generate an NSF-‐style collaborative proposal for original research on a specific group of organisms (e.g., eel larvae, spiny lobster larvae, microbes, Sargassum community). The proposal will include a thorough introduction to the subject, statement of a research question and hypothesis, and a detailed account of proposed experimental methods and data analysis techniques. All collaborative research



projects will result in one Final Research proposal; for joint work, all students earn the same grade.

Peer/Self Evaluation of Team Contribution: Candid self and peer evaluations of research project contributions will be completed. Emphasis will be placed on identifying individual strengths and weaknesses in the context of collaborative work. Expectations and Requirements:

• Punctual attendance is required at every class meeting. • Active participation in class discussion is expected. • Late assignment submissions are not accepted. • The policy on academic accuracy, quoted below, will be strictly followed in this class.

The papers that you submit in this course are expected to be your original work. You must take care to distinguish your own ideas and knowledge from wording or substantive information that you derive from one of your sources. The term “sources” includes not only published primary and secondary material, but also information and opinions gained directly from other people and text that you cut and paste from any site on the Internet. The responsibility for learning the proper forms of citation lies with you. Quotations must be placed properly within quotation marks and must be cited fully. In addition, all paraphrased material must be acknowledged completely. Whenever ideas or facts are derived from your reading and research, the sources must be indicated. (Harvard Handbook for Students, 305)

• Considerations for use of internet sources: As you browse websites, assess their usefulness very critically. Who posted the information and why? Can you trust them to be correct? Authoritative? Unbiased? (It’s okay to use a biased source as long as you incorporate it knowingly and transparently into your own work.) Keep track of good sources that might be useful for subsequent assignments, and annotate in your bibliography any sites you cite. Your annotation should include the name of the author or organization originating any material that you reference. If you can’t identify the source, don’t use it!

Required Readings: Appeltans W et al. 2012. The magnitude of global marine species diversity. Current Biology 22:

1-‐14. Bucklin A et al. 2010a. A “rosetta stone” for metazoan zooplankton: DNA barcode analysis of

species diversity of the Sargasso Sea (Northwest Atlantic Ocean). Deep-‐Sea Research II 57: 2234-‐2247.

Bucklin A et al. 2010b. A census of zooplankton of the global ocean. In: Life in the World’s Oceans. AD McIntyre [ed]. Wiley-‐Blackwell, 384 pp.

Hamilton MB. 2009. Population Genetics. Wiley-‐Blackwell, 424pp. Laffoley Dd’A et al. 2011. The protection and management of the Sargasso Sea: The golden

floating rainforest of the Atlantic Ocean. Summary Science and Supporting Evidence Case. Sargasso Sea Alliance, 44 pp.

Lomas MW et al. (eds) 2011. Oceanography of the Sargasso Sea: Overview of Scientific Studies. Sargasso Sea Alliance Science Report Series, No 5, 64 pp.



Magurran AE and BJ McGill [eds.] 2011. Biological diversity: frontiers in measurement and assessment. Oxford University Press, Inc. New York. 345pp.

McManus GB and L Katz. 2009. Molecular and morphological methods for identifying plankton: what makes a successful marriage? J Plankton Research 31: 1119-‐1129.

Pedros-‐Alio C. 2006. Marine microbial diversity: can it be determined? Trends in Microbiology 14: 257-‐263.

Segar DA. 2007. Introduction to Ocean Sciences, 2nd Edition. W.W. Norton & Company, New York. 581 pp.

Snelgrove PVR. 2010. Discoveries of the Census of Marine Life: making ocean life count. Cambridge University Press. 286 pp.

Solow AR. 1995. Estimating biodiversity: calculating unseen richness. Oceanus 38: 9-‐10. Solow AR and D Tittensor. 2010. The sea, the Census and statistics. Significance 7: 155-‐158. Spalding MD et al. 2012. Pelagic provinces of the world: a biogeographic classification of the

world’s surface pelagic waters. Ocean & Coastal Management 60: 19-‐30. Tittensore DP et al. 2010. Global patterns and predictors of marine biodiversity across taxa.

Nature 466: 1098-‐1101. Ullman DS et al. 2007. On the characteristics of subtropical fronts in the North Atlantic. J.

Geophysical Research 112: C01010. Webb TJ et al. 2010. Biodiversity’s big wet secret: the global distribution of marine biological

records reveals chronic under-‐exploration of the deep pelagic ocean. PLoS One 5: e10223.



Course Calendar: Topic Readings/Assignments Due Week 1 (12.25 hrs) MBC Program Goals and Expectations Science and Policy Research Orientation Oceanography of the Sargasso Sea

Sargassum and the Sargassum Community MBL Library Orientation Measuring Biodiversity

Diversity Indices Software Lab Interdisciplinary Seminar: Species Concept

Select Interdisciplinary Seminar Topic Cruise Prospectus; Proposal Writing Guidelines Select Biodiversity Research Area Segar p. 177-‐185, p. 207-‐228; Lomas et al. 2011 Ch. 1-‐4; Ullman et al. 2007 Laffoley et al. 2011 Magurran and McGill 2011, Ch.6; Solow 1995; Solow and Tittensor 2010

Diversity Indices Lab Duehj Selected Readings

Week 2 (15.25 hrs) Marine Biodiversity Status Report

OBIS Workshop Marine Plankton Taxonomy/Identification Classical Taxonomy Lab BIOD Research Group Meeting I Marine Protection Case Study: Mediterranean Interdisciplinary Seminar: Baselines

Snelgrove 2010, Ch. 1; Appeltans et al. 2012; Webb et al. 2010 ; Tittensor et al. 2010 OBIS Assignment Due Taxonomy Lab Due BRGM Assignment I Due Selected Readings Selected Readings

Week 3 (16.75 hrs) Population Genetics Molecular Tools Workshop

• DNA extraction and amplification Field Trip: MBL Sequencing Facility BIOD Research Group Meeting II Marine Protection Case Study: Barents Sea, Norway Marine Protection Case Study: Stellwagen Bank Interdisciplinary Seminar: Defining Boundaries

Hamilton 2009, Chpts. 1-‐2 BRGM Assignment II Due Selected Readings Selected Readings Selected Readings

Week 4 (11.75 hrs) BIOD Final Exam BIOD Research Group Meeting III Guest Lecture: Census of Marine Zooplankton Guest Lecture: Marine Ciliate Diversity Research Proposal Presentations Interdisciplinary Seminar: Genetic Resources

BRGM Assignment III Due Bucklin et al. 2010a; Bucklin et al. 2010b

McManus & Katz 2009; Pedros-‐Alio 2006 hj Research Proposal Due Selected Readings



Topic Readings/Assignments Due Week 5 (1 hr, at sea) Bermuda Geology Selected Readings

Week 6 (1 hr, at sea) Bermuda Reef Ecology Selected Readings

Week 7 (8 hrs, Bermuda port stop) Field Trip -‐ Bermuda Institute of Ocean Science

• Facility Tour • Lecture – Bermuda Atlantic Time Series • Lecture – Marine Debris on Bermuda Beaches

Field Trip -‐ Bermuda Aquarium, Museum and Zoo • Behind the Scenes Tour (Aquarium and

Veterinary Facilities) • Snorkel Trip – Bermuda Coral Reefs

Week 9 (4 hrs, New York port stop) Field Trip -‐ New York Aquarium & Wildlife Conservation Society

• Facility Tour • Lecture – NY Seascape

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Syllabus Advanced Topics in Biological Oceanography MBC€¦ · SEA$Semester®:$Marine$Biodiversity$&$Conservation$ $$$$$AdvancedTopics$inBiological$Oceanography:$Biodiversity$A$1$