Marine Ecology (Biology 474/574) Summer 2015 Instructor: Teaching Assistant: Class meeting times: Class website: Office hours: Required materials:

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Darren Nicholson
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1 Marine Ecology (Biology 474/574) Summer 2015 Oregon Institute of Marine Biology, University of Oregon Instructor: Ben Grupe (please no text messages) Teaching Assistant: Anders Hansen Class meeting times: MWF 8:00 AM 4:50 PM (but finishing at 3:20 on Wednesdays), with occasional EARLIER start times based on tides Class website: blackboard.uoregon.edu/ Office hours: I do not have formal office hours, but will meet with you outside of class time if you speak with me to set up a time. I ll usually be around campus Tuesday, Thursday, and after class. Anders works after class, but is available on Tuesday and Thursday, including evenings. Required materials: Waterproof field notebook (Rite in the Rain) and pencil for field trips Rubber boots (knee- high) or hip waders, and rain gear when necessary Tide chart (either digital or a pocket calendar) A dissection kit will come in handy, though isn t absolutely required Books: You should have a copy of Seashore Life of the Northern Pacific Coast, by Eugene Kozloff. It will allow you to begin to become accustomed to particular habitats, so you are asked to read chapters on various environments BEFORE the associated field trips. (And read chapter 2 immediately if you haven t already taken invertebrate zoology!) There is NO required textbook for this class. There are, however, several very nice marine ecology texts easily available that you may be interested in acquiring, especially if you plan to continue in marine ecology for graduate studies. Some of these (and others) will be placed on reserve in the OIMB library. (See list at end of syllabus.) Course objectives: Marine ecology involves the various factors that influence the abundance, distribution, and diversity of organisms in different marine ecosystems, including effects of anthropogenic impacts that are becoming increasingly more pervasive. Given our location, we will emphasize aspects of marine ecology that relate to the incredible diversity of habitats that can be found on the southern Oregon coast (exposed and protected rocky shores, sandy beaches, estuarine environments, sand dunes, planktonic assemblages, etc.). The major goals of this course will be to: 1) Become familiar with common themes in marine ecology relating to patterns of primary and secondary production, important ecological interactions, and structurally and functionally important taxa in different marine environments; 2) Perform ecological surveys to become familiar with local marine habitats, and foster an appreciation for the natural history of the marine habitats of the southern Oregon coast 3) Learn and practice common quantitative field sampling techniques, including data collection, data visualization, statistical analysis, and ecological interpretation; 4) Discuss scientific literature that elucidates the themes in marine ecological research highlighted in all aspects of the course; 5) Gain research experience in marine ecology through the design, execution, and written and oral communication of individual research projects. My teaching philosophy: This is an intensive field, lab, and lecture course that is designed for upper- division undergraduate students in biology- related majors. Accordingly, more will be expected of students than in your typical university lecture course (you are receiving 8 credits, after all!) Please let us know as soon as possible if you find that you are having trouble with any aspect of the course. You will participate in many learning activities including lectures, group activities, field trips, data collection and analysis of data, quizzes, individual and group presentations, discussions of papers from the scientific literature, and workshops on various aspects to familiarize you with learning to do ecology. As such, we will emphasize observational and questioning skills, the ability

2 to critically think about the research of yourself and other scientists, and the ability to communicate your research orally and in writing. Active participation is expected, as is regular attendance. Grading: Research project: 40% (Percentages are approximate proposal, presentation, report and subject to change.) Participation and in- class activities 15% Reading assignments and write- ups 20% Field notenook 5% Quizzes 10% each) 20% Research project: A major component of this course is a research project that YOU will design, conduct, analyze data you collect, and ultimately communicate as an oral presentation and formal scientific report. Your project can be related to any topic in marine ecology, but it is expected to original and independent. Begin thinking right away about what your project might entail. There will be several checkpoints intended to allow you to receive feedback throughout the process. Oral presentation of proposed research Wednesday July 8 Methods discussion with Ben and Anders during week of July Data discussion with Ben and Anders On or before August 4 Oral research report August 10 Final paper due August 13 by 5:00 P.M. Readings and paper discussions: Readings are often meant to complement lectures, and are usually best read before the lecture. Some readings from the scientific literature will be assigned. These will usually be made available as PDFs on the Blackboard website. An important part of being a scientist is being able to read and evaluate published literature, thinking critically about the merits of the research being discussed. Thus, we will set aside some class time for discussions of specific papers, and groups of students will take turns leading discussions. Quizzes: There will be two quizzes (July 15 and August 7). These are intended to assess your learning from lectures, field trips, lab activities, readings, and discussions. Questions will usually be short answer, but may include essays. Field notebook: You are expected to keep notes during field trips in your Rite in the Rain notebooks. Use a pencil so that there is no chance of ink running should it get wet. You should record your observations while you are in the field, because most memories are not good enough to remember accurate details once you have left. Note are for your benefit, but also for other scientist, in case someone wished to duplicate your research at some point in the future. As such, you need to include certain important details such as: - Location (enough detail that someone else could find your site perhaps including Latitude/Longitude or a rough map of your study area/site) - Date and Time (use the 24 hour time clock to avoid confusion) - Description of the habitat (mainly the habitat in which you are observing plants and animals, but it may be useful to take notes on your surroundings as well) - - Weather Observations and data collected (in such a way your work could be repeated). You might also record questions, hypotheses, or sudden thoughts of brilliance that come to you while staring at a sea star. You never know when inspiration will strike. just be certain to keep your objective observations and data separate from your editorial comments and suppositions I do not plan to review your notebooks in detail, but I will ask to see them once or twice during the class, just to make sure you are keeping detailed notes during each trip.

3 Academic honesty I expect that you ll all conduct yourselves appropriately and will seek to avoid any situations that could be construed as cheating or plagiarism. Still, you should know that I take all issues of academic dishonesty very seriously. In these cases, assignments, papers, or exams will receive a grade of 0, and I will follow the university s policy with regard to possible additional penalties. Schedule This gives you a general idea of the range of topics and types of field experiences that will be involved in this course. The schedule will change in order to optimize class dynamics, but you will have at least a few days of lead time on changes. These will be announced in class and posted on Blackboard. Week 1 Low Tide Mon, June 22 Introduction to Marine Ecology :51 FIELD TRIP Sunset Bay rocky intertidal: observations and patterns Literature research and using the OIMB library Brief presentations of field observations and library research Wed, June 24 Philosophy of Science lecture and workshop :21 Discuss Platt reading Introduction to fouling communities FIELD TRIP Charleston boat basin fouling communities and student observations 4:00 Seminar Scott Heppell (Nassau grouper recovery) Fri, June 26 Geography, climate, and oceanography of the Pacific Northwest :07 Lab review of basic graphing and stats (Excel) using dock data FIELD TRIP to Metcalf Marsh. Quantitative measurements of organism density Readings: Schultz Northwest natural history chapter, Komar chapters 1-3, Kozloff chapters on instant zoology and docks & pilings Week 2 Mon, June 29 Marine vs Terrestrial environments :08 Context of the marine physical environment and abiotic factor activity Discussion of Friday s marsh data Seaweeds and algae Group discussion and presentations on abiotic factor research Readings: Denny & Gaylor 2002, Helmuth et al 2006, Smetacek 2012 Kozloff chapters on instant botany, rocky shores of Puget Sound region (peruse) Wed, July 1 FIELD TRIP Middle Cove (6:00 AM) :30 Quantifying intertidal community structure (algae focus) Algae identification in lab Discuss Bertness & Hacker (1994) 4:00 Seminar Nancy Treneman (boring shipworms) Reading: Kozloff chapter on rocky shores of open coast Fri, July 3 FIELD TRIP Cape Blanco (6:00 AM) :52 Algae identification in lab Time to meet with student to discuss projects Seaweed and algae pressing (Optional Sunday activity) Reading: Kozloff chapter on rocky shores of open coast (if not finished) Week 3 Mon, July 6 Primary productivity - 10:02 AM Free time to work on individual research projects Optional field trip to mudflats for students interested in that environment Data analysis of Cape Blanco intertidal data Discuss lab write- up (due 7/24)

4 Wed, July 8 Research Proposals oral presentations 11:41 Secondary productivity 7:00 p.m. Seminar Kelly Sutherland Fri, July 10 Bottom- up versus Top- down forcing 13:41 Terrestrial versus Marine food webs Discussion of Baum & Worm (2009) and Beaugrand et al. (2003) Reading: Shurrin et al. 2006, Webb 2012 Week 4 Mon, July 13 Review for Quiz - 5:04 Introduction to pervasive ecological themes in the rocky intertidal, classic studies, and indirection interactions Jigsaw on indirect interaction readings (Dayton 1973, Raimondi et al. 2000, Trussell et al. 2003, Wootton 1992) Read: Connell 1961, Paine 1971 Wed, July 15 AM - Free time to work on individual research projects (field work) - 6:34 Introduction to soft sediments, sandy beaches Lab activity on sandy beach communities Quiz 1 4:00 Seminar Ben Grupe (methane seep communities) Reading: Kozloff chapter on sandy beaches, protected Fri, July 17 FIELD TRIP Bastendorff beach, Emerita population sampling - 7:50 Lab activity Emerita data analysis Larval ecology Deadline to discuss your research methodology with Ben and Anders Read: Kozloff chapter on sandy beaches, exposed Week 5 Mon, July 20 AM - Free time to work on individual research projects 9:34 Larvae and Population Connectivity Group project on population connectivity in a coastal species Wed, July 22 Group presentations on coastal species population 10:45 Discuss Harmon et al and sea star wasting, marine disease Coral reefs 4:00 Seminar Rebecca Vega- Thurber (coral microbes) Fri, July 24 Coastal ecosystems: tropical versus temperate 12:13 Fisheries and overfishing, discussion Marine reserve class interactive simulation Read: Pauly et al. 1998, Jackson et al Week 6 Mon, July 27 Introduction to the deep sea: adaptations and ecology 3:49 ROV Nautilus expedition (online telepresence at a methane seep) Select papers for group discussions Chemosynthetic habitats: vents, seeps, and whale falls Free time to work on individual research, graphing Wed, July 29 Biodiversity patterns and metrics of biodiversity - 5:23 ROV Nautilus real time data collection and biodiversity analysis Student- led paper discussion Biodiversity and Ecosystem Function Papers TBA 4:00 Seminar Luiz Rocha (tropical fish) Evening optional viewing of whale fall ROV dive Fri, July 31 FIELD TRIP Dome house mudflat and eelgrass - 6:48 Free time for field work or data consultations individual research Invasive species

5 Fri, July 31 (continued) Student- led paper discussion invasions Papers TBA Discuss data from mudflat field trip Time for individual data consultation with Ben Read: Kozloff, quiet bays and salt marshes (if you haven t already!) Week 7 Mon, Aug 3 AM - Free time to work on individual research - 8:54 Climate change and marine ecology Student- led paper discussion Ocean acidification Papers TBA Time for individual data consultation with Ben Tue, Aug 4 Deadline to discuss your data with Ben and Anders Wed, Aug 5 FIELD TRIP Restoration ecology in South Slough 10:24 Student- led paper discussion Restoration ecology Papers TBA Discussion: Applying to graduate school 4:00 Seminar Leif Rasmuson (Ph.D. Defense) Fri, Aug 7 Quiz 2 12:14 Science communication workshop PM Free time to work on individual research; Optional dunes field trip Week 8 Mon, Aug 10 Marine Ecology Research Symposium (All day) - 3:54 Wed, Aug 12 Peer editing, writing tips - 5:33 Free time to write research papers Writing consultations with Ben and Anders 4:00 Seminar OIMB Grad Students (deep- sea expedition) Thur, Aug 13 Paper due at 5:00 P.M. Fri, Aug 14 Clean lab at 9:00 A.M. Required class day - 6:50 Textbooks in marine ecology (not required): Marine Ecology: Processes, Systems, and Impacts, Kaiser et al., 2011, 2 nd edition, Oxford Press There are several other basic marine ecology textbooks. What I like about this one is that it is more worldly (less American- centric) than other texts, it has a nice division of chapters, and it dedicates a good portion of the book to human impacts, which is probably where many of you are likely to interact with the field of marine ecology most frequently. Marine Biology: Function, Biodiversity, Ecology, Levinton, 2013, 4 th edition, Oxford Press A nice background text if you simply want to have a better knowledge of various types of marine organisms, their function, and how they relate to themes in marine ecology. Marine Community Ecology and Conservation, Bertness et al. 2014, Sinauer Marine Community Ecology, Bertness et al., 2001, Sinauer These texts are especially recommended for future graduate students in marine ecology. The 2001 book is an excellent synopsis of the major themes in marine community ecology, and is still really considered the gold standard for review papers on many of these topics. The 2014 book is slightly updated, though it s main purpose it to introduce and expand on themes of conservation while still including the most basic themes from the first textbook. Other recommended books: Between Pacific Tides, Ed Ricketts (5 th edition, 1992) This really is a must- own if you have serious interest in marine biology, the ecology of marine nearshore habitats, or enjoy learning natural history factoids relating to the most common species from the west coast intertidal.

6 The Log from the Sea of Cortez, John Steinbeck This narrative recounts Steinbeck and Ricketts month long collecting expedition in the Gulf of California in An exciting day- by- day account of their journey together is a rare blend of science, philosophy, and high- spirited adventure, this is a great read for tidepool explorers and travelogue junkies. Beachcomber s Guide to Seashore Life in the Pacific Northwest (revised), J Duane Sept Contains illustrations of 274 of the most common plants and animals in the Pacific Northwest. Encyclopedia of Tidepools and Rocky Shores, Mark Denny & Steve Gaines, 2007 An authoritative encyclopedia, too huge to read cover- to- cover, but providing an excellent overview on many marine taxa, ecological themes, and nearshore marine environments.

Oregon Institute of Marine Biology

Reprinted from BULLETIN OF THE ECOLOGICAL SOCIETY OF AMERICA Vol. 78, No. 2, April 1997 Made in United States of America The Oregon Institute of Marine Biology Introduction Oregon Institute of Marine Biology