Course Info

Time:              TTh 2-3:30, Lab W 8 -11 or tide dependent

Classroom:      Lecture – University Hall Y04-4190, Lab – McCormack 01-0318 or otherwise (see schedule)

Instructor and TA emails: jarrett.byrnes@umb.edu and Michael.Roy002@umb.edu

Instructor Office Hours: Wednesdays 2-3:30, ISC 3130

TA Office Hours: Tuesdays 10-11, Thursday 3:45-4:45

Instructor Office Location: ISC-3-3240

Syllabus: Lecture, Lab

Midterm: Due Oct 13th. See this handout for details.

Marine Biology & Ecology will explore the diversity of biological and ecological processes that shape life in the oceans. We will place a special emphasis on marine life in New England, focusing on the interactions between humans and the sea. This focus will lead to a greater understanding of the consequences of ongoing environmental changes in the 20th and 21st centuries.

Resources and Links

Full Syllabus on Word format

Course Schedule

Week 1. Topic: Intro, Physical processes in marine biology, How to read a Scientific Paper

Objective(s): Understand how physics of moving water influence marine biological processes. Demystify reading the scientific literature

Textbook Readings: MCEC Ch. 2

Journal Readings: Siddon and Witman 2003

Resources: How to read scientific papers, Anatomy of a Scientific Paper


Week 2. Topic: Dispersal

Objective(s): Evaluate multiple perspectives on the importance of physical versus biological forces in the dispersal of marine larvae; learn what makes for an effective paper discussion

Textbook Readings: MCEC Chapter 4

Journal Readings: Gaines and Roughgarden 1985, Morgan et al 2008

Lab: Diversity and distribution of fouling organisms: Handout, species IDs. Meet at the Fox Point Pavilion by the docks!


Week 3. Topic: Predation & Herbivory

Objective(s): Discover that the seemingly simple species interactions of predation and herbivory can lead to a variety of non-intuitive effects

Textbook Readings: MCE Chapter 5

Journal Readings: Stachowicz and Hay 1999, Matassa and Trussell et al. 2011

Blog Posts of Note: Dragons, Sea Urchins, and Sea Otters? Oh my!

Lab:Experimental design and basics of data analysis. For more on pivot tables, see here and here. These are for google sheets, but all works roughly the same if you use excel.

Week 4. Topic: Pelagic Communities

Objective(s): Learn how energy and nutrients move through the open ocean, from phytoplankton to tuna.

Textbook Readings: MCEC Chapters 15-16

Journal Readings: Stibor et al. 2004, Worm et al. 2005

Other Assignments: Midterm Papers due on Friday

Lab: Amphipod Habitat Choice

Week 5. Topic: The Rocky Intertidal

Objective(s): Understand how and why the rocky intertidal is the workhorse model system for testing ideas in marine ecology.

Textbook Readings: MCE Chapter 9

Journal Readings: Paine 1974, Nielsen and Navarette 2004

Lab: Rocky intertidal zonation and facilitation. Meet at the back of the Bayside lot at 6am!


Week 6. Topic: Salt Marshes

Objective(s): Understand differing perspectives on what controls salt marsh zonation. Confront a current controversy into why we are witnessing widespread salt-marsh dieback.

Textbook Readings: MCE Chapter 11

Journal Readings: Deegan et al. 2012, Altieri et al. 2012

Lab: Wednesday Oct 11th – salt marsh community structure. Saturday Oct 14th, Plum Island field trip! Details forthcoming.

Week 7. Topic: Microbial Processes

Objective(s): In the opinion of some, microbes rule the world. Why have we only begun how important they are in marine processes? What role do they play?

Textbook Readings: Azam and Malfatti 2007, Breitbart 2012

Journal Readings: Bowen et al. 2009, Marston et al. 2012

Lab: No Lab!


Week 8. Topic: Seagrass Beds

Objective(s): Begin to think about coastal ecosystems as complex systems that can be altered from outside impacts.

Textbook Readings: MCEC Chapter 12

Journal Readings: Irlandi and Peterson 1991, Whalen et al. 2012

Other Assignments: Final Project Proposals Due


Week 9. Topic: Coral Reefs

Objective(s): Incorporate an understanding of how complex symbioses and the micro- and macro- level can lead to a fully functional ecosystem.

Textbook Readings: MCEC Chapter 29

Journal Readings: Rowan et al. 1997, Burkepile and Hay 2008


Week 10. Topic: Kelp Forests

Objective(s): Incorporate thinking about the multiple ecosystem functions that foundation species provide.

Textbook Readings: MCEC Chapter 14

Journal Readings: Arkema et al. 2009, O’Brien et al. 2015


Week 11. Topic: Shifting Baselines and Marine Historical Ecology

Objective(s): Learn to think in terms of historical and deep time in order to understand present-day ocean ecosystems.

Textbook Readings: MCEC Chapter 8

Journal Readings: Steneck 2013

Week 12. Topic: Ocean Ecosystem Services

Objective(s): Build an appreciation for the ways humans benefit from ocean ecosystems.

Textbook Readings: MCEC Chapter 18

Journal Readings: MacLeod et al. 2011, Barbier et al. 2013

Week 13. Topic: Extinction, Biodiversity, and Ecosystem Function

Objective(s): Understand why species diversity and the global extinction crisis matters to the future of functional ocean ecosystems.

Textbook Readings: MCEC Chapter 6

Journal Readings: Duffy et al. 2003, Best et al. 2014


Week 14. Topic: Climate Change

Objective(s): Understand the connections between human activities, changes in climate cycles, and how this is likely to alter the biology of oceans in the future.

Textbook Readings: MCEC Chapter 19

Journal Readings: Harley 2011, Poloczanska et al. 2013


Week 15. Topic: Fisheries and Ocean Management

Objective(s): Debate and arrive at solutions for maintaining functioning ocean ecosystems that provide humans with a wide variety of goods and services.

Textbook Readings: MCEC Chapter 20

Journal Readings: Myers & Worm 2003, White et al. 2012


Required Assignments:

Regular Essays: I realize that for some of you this class is your first encounter to the primary literature, and it can be a bit daunting. As such, we’re going to change the weekly assignment to help you make sure you’ve fully understood the reading and can begin to dig into it intellectually before class.

For each class we have scientific papers assigned, choose one of the papers assigned and in 1-1.5 pages, no more, in 12 point single spaced font. Answer the following four questions:

1) Why are the authors writing this paper? What larger body of ideas does it sit within?
2) What were their hypotheses, and how did they test them?
3) What did their findings teach them about their questions or ideas of interest?
4) Are you persuaded by what they have done? Why or why not?

Feel free to also discuss any insights you have about the work presented from outside of class. Many of the papers we read will revolve around the natural history of New England. Were there any particular points of connection that this paper made with your own experiences? Did it make you think about any particular issue differently?

Essays will be marked as completed or not. Essays that provide no more detail than the abstract of the paper will be marked as not completed.

Midterm Paper: There are two options.

Option 1 – I came here for an argument: Students will select one pair of papers from a list of papers that famously disagreed with one another. Students should read the papers and at minimum 3 associated papers from the reference list to understand its context and 2 papers that cite it (use Google Scholar). Students are then asked to write a short persuasive essay (5 pages max.) that 1) summarizes the papers main arguments, 2) states compares and contrasts the differing points of view, 3) argues which one got it right.

Option 2 – North versus South: When the first edition of Marine Community Ecology by Bertness et al. came out, a parallel text by Australian researchers was also published. The two differ greatly in focus of examples, papers cited, and authors of chapters. The current edition has much more back and forth between the southern and northern hemisphere. Read one chapter from the first edition, it’s parallel from the Australian Marine Ecology (Connell et al. eds), and write a short essay (5 pages max) that 1) compares and contrasts the two chapters, 2) elucidates what is gained by taking a broader perspective across multiple academic groups, and 3) discusses whether there is generality to the principles in either text or if local examples cannot be generalized. Students may also explore how the 2nd edition of Bertness et al. synthesizes these two points of view. Students should also explore the original references (at least 2-3) cited by the chapters.

Students will be graded equally on their accuracy, understanding of the material discussed, the strength of their argument, and the style of their writing. Grammar and spelling count. Students will be given an opportunity to revise and resubmit.


Final Project: Students have the choice of either taking a final written exam during the exam period or presenting a final interdisciplinary project. As students are entering the course with varying backgrounds and interests, the interdisciplinary project is designed for students to address the course material using their own perceived strengths – even if they are outside of the scope of a formal marine science education. Interdisciplinary projects can take several forms: 1) a grant proposal for future work complete with preliminary data from the literature, 2) a film (animation, music video, documentary, etc.) exploring a paper or theme from class,

See http://www.youtube.com/user/iambient33 and http://creaturecast.org/ for examples 3) a piece of original research with accompanying writeup ranging from taking data in the field, from online databases (e.g., http://marinexplore.org), building a new sensor or marine tool (e.g., SeaPerch ROV), a survey of people regarding attitudes or knowledge of relevant issues, etc. 4) other piece of creative work. Projects falling outside of these areas but demonstrating a connection between the course material and the students’ knowledge are essential. Projects other than the grant proposal can be done in groups. All projects must be approved by the Professor by November 1st. Projects will be graded on a demonstration of mastery and understanding of topic material in the context of the work. Projects will be presented to the class at large on the last day of classes.

Leading a Discussion: Throughout the semester students will be asked to lead 1-2 discussions of academic papers.


Text:           MCEC: Bertness, M.D., Bruno, J.F., Silliman, B.R., and Stachowicz, J.J. eds. 2014. Marine Community Ecology and Conservation. Sinauer Associates. 978-1-60535-228-2

Other  Reading:        MCE: Some readings will be photocopied and distributed from the out of print Bertness, M.D., Gaines, S.D., and Hay, M.H. eds. 2001. Marine Community Ecology. Sinauer Associates.


Recommended Texts               If you wish to review relevant material before beginning this course, I recommend Levinton, J.S. 2013. Marine Biology, 4th Edition. Oxford University Press.


Altieri, A. H., M. D. Bertness, T. C. Coverdale, N. C. Herrmann, and C. Angelini. 2012. A trophic cascade triggers collapse of a salt-marsh ecosystem with intensive recreational fishing. Ecology 93:1402–1410.

Arkema, K. K., D. C. Reed, and S. C. Schroeter. 2009. Direct and indirect effects of giant kelp determine benthic community structure and dynamics. Ecology 90:3126–3137.

Barbier, E. B., I. Y. Georgiou, B. Enchelmeyer, and D. J. Reed. 2013. The Value of Wetlands in Protecting Southeast Louisiana from Hurricane Storm Surges. PloS one 8:e58715.

Best, R. J., A. L. Chaudoin, M. E. S. Bracken, M. H. Graham, and J. J. Stachowicz. 2014. Plant–animal diversity relationships in a rocky intertidal system depend on invertebrate body size and algal cover. Ecology 95:1308–1322.

Bowen, J. L., B. C. Crump, L. A. Deegan, and J. E. Hobbie. 2009. Increased supply of ambient nitrogen has minimal effect on salt marsh bacterial production. Limnology and Oceanography 54:713–722.

Breitbart, M. 2012. Marine Viruses: Truth or Dare. Annual Review of Marine Science 4:425–448.

Burkepile, D. E., and M. E. Hay. 2008. Herbivore species richness and feeding complementarity affect community structure and function on a coral reef. Proceedings of the National Academy of Sciences of the United States of America 105:16201–16206.

Deegan, L. A., D. S. Johnson, R. S. Warren, B. J. Peterson, J. W. Fleeger, S. Fagherazzi, and W. M. Wollheim. 2012. Coastal eutrophication as a driver of salt marsh loss. Nature 490:388–392.

Duffy, J. E., J. P. Richardson, and E. A. Canuel. 2003. Grazer diversity effects on ecosystem functioning in seagrass beds. Ecology letters 6:637–645.

Gaines, S., and J. Roughgarden. 1985. Larval settlement rate: A leading determinant of structure in an ecological community of the marine intertidal zone. Proceedings of the National Academy of Sciences of the United States of America 82:3707–3711.

Glover, A. G., H. Wiklund, S. Taboada, C. Avila, J. Cristobo, C. R. Smith, K. M. Kemp, A. J. Jamieson, and T. G. Dahlgren. 2013. Bone-eating worms from the Antarctic: the contrasting fate of whale and wood remains on the Southern Ocean seafloor. Proceedings of the Royal Society B: Biological Sciences 280:20131390–20131390.

Harley, C. D. G. 2011. Climate Change, Keystone Predation, and Biodiversity Loss. Science 334:1124–1127.

Irlandi, E. A., and C. H. Peterson. 1991. Modification of animal habitat by large plants: mechanisms by which seagrasses influence clam growth. Oecologia 87:307–318.

Ling, S. D., C. R. Johnson, S. D. Frusher, and K. R. Ridgway. 2009. Overfishing reduces resilience of kelp beds to climate-driven catastrophic phase shift. Proceedings of the National Academy of Sciences 106:22341–22345.

Matassa, C. M., and G. C. Trussell. 2011. Landscape of fear influences the relative importance of consumptive and nonconsumptive predator effects. Ecology 92:2258–2266.

Mcleod, E., G. L. Chmura, S. Bouillon, R. Salm, M. Björk, C. M. Duarte, C. E. Lovelock, W. H. Schlesinger, and B. R. Silliman. 2011. A blueprint for blue carbon: toward an improved understanding of the role of vegetated coastal habitats in sequestering CO2. Frontiers in Ecology and the Environment 9:552–560.

Morgan, S. G., and J. R. Anastasia. 2008. Behavioral tradeoff in estuarine larvae favors seaward migration over minimizing visibility to predators. PNAS 105:222–227.

Myers, R. A., and B. Worm. 2003. Rapid worldwide depletion of predatory fish communities. Nature 423:280–283.

O’Gorman, E. J., R. A. Enright, and M. C. Emmerson. 2008. Predator diversity enhances secondary production and decreases the likelihood of trophic cascades. Oecologia 158:557–567.

Paine, R. T. 1974. Intertidal community structure. Oecologia 15:93–120.

Poloczanska, E. S., C. J. Brown, W. J. Sydeman, W. Kiessling, D. S. Schoeman, P. J. Moore, K. Brander, J. F. Bruno, L. B. Buckley, M. T. Burrows, C. M. Duarte, B. S. Halpern, J. Holding, C. V. Kappel, M. I. O’Connor, J. M. Pandolfi, C. Parmesan, F. Schwing, S. A. Thompson, and A. J. Richardson. 2013. Global imprint of climate change on marine life. Nature Climate Change:–.

Rowan, R., N. Knowlton, A. Baker, and J. Jara. 1997. Landscape ecology of algal symbionts creates variation in episodes of coral bleaching. Nature 388:265–269.

Siddon, C. E., and J. D. Witman. 2003. Influence of chronic, low-level hydrodynamic forces on subtidal community structure. Marine Ecology Progress Series 261:99–110.

Stachowicz, J. J., and M. E. Hay. 1999. Reducing predation through chemically mediated camouflage: Indirect effects of plant defenses on herbivores. Ecology 80:495–509.

Stibor, H., O. Vadstein, S. Diehl, A. Gelzleichter, T. Hansen, F. Hantzsche, A. Katechakis, B. Lippert, K. Loseth, C. Peters, W. Roederer, M. Sandow, L. Sundt-Hansen, and Y. Olsen. 2004. Copepods act as a switch between alternative trophic cascades in marine pelagic food webs. Ecology letters 7:321–328.

White, C., B. S. Halpern, and C. V. Kappel. 2012. Ecosystem service tradeoff analysis reveals the value of marine spatial planning for multiple ocean uses. PNAS 109:4696–4701.

Worm, B., M. Sandow, A. Oschlies, H. K. Lotze, and R. A. Myers. 2005. Global Patterns of Predator Diversity in the Open Oceans. Science 309:1365–1369.