W4110 Coastal & Estuarine Ecology
1009 Schermerhorn Ext.
E-mail: [email protected]
Email: [email protected]
Meeting Time: Monday and Wednesdays: 11:40am-12:55pm
Office Hours: Wednesday 10:30-11:30am or by appointment
Introduction to Physical Oceanography by Robert H. Stewart (free PDF: http://www.colorado.edu/oclab/sites/default/files/attached-files/stewart_textbook.pdf)
Recommended: Marine Community Ecology and Conservation by Mark Bretness et al.
Course Objective: to understand the physical, chemical, and biological influences that create the diversity of near shore environments.
Mid-Semester Lecture Exam 1 @ 100 points 100
Assignments 3 @ 50 points each 150
Lecture Final 1 @ 100 points 100
Term Paper 1 @ 100 points 100
Discretionary / Participation Points 50
Total 500 points
Mid Semester and Final Exams:
For each lecture exam, you will be responsible for all reading and lecture materials. The final exam is comprehensive, but will be weighted for material after the mid-semester exam. If you have a conflict with exams, contact me as soon as possible: arrangements may be made to take the exam prior to the scheduled date. There are no make-ups for missing an exam, unless you have a valid, pre-approved excuse, medical emergency, etc.
Credit may be given to students who willingly participate in class discussions and Classroom Assessment Techniques (C.A.T.s). No other extra credit points will be available.
In order to assure the class is progressing on schedule and concurrent with our expectations, we will regularly ask students to complete Classroom Assessments (or C.A.T.s). C.A.T.s are simple, non-graded, anonymous, in-class activities designed to give us feedback on the teaching-learning process as it is happening. These will range from defining principles or explaining lecture content in a few sentences, to identifying areas of heightened importance or confusion.
Assignment 1: Trip to AMNH
We will be taking a trip to the American Museum of Natural History where students will learn about the value of collections and understand the various ways they can help us understand the ecology of marine systems. The trip assignment will consist of a scavenger hunt which students will have one week to complete, and for graduate students a written reflection and small literature search on the history of a particular item in the collection (1000 words).
Assignment 2: Documentary Analysis Presentation:
We will be assessing environmental documentaries as an exercise. Each Monday, one pair of students will present on a documentary they have watched that dealt with some aspect of coastal and estuarine ecology. The pair must provide the title of the documentary at least one week in advance so that the class as a whole can watch the video before the presentation on Monday (choosing videos that are available online, or on Netflix, Amazon Prime, etc. will help facilitate the class’ viewing and discussion). Each pair will present the documentary to the class, explaining 1) the positive qualities of the documentary (ex. strategies they used to engage the audience, truthfulness of their message, etc.), 2) where it needed improvement, and 3) if any biases were introduced by the directors. Each student in the pair should think about these points independently: this will allow you to discuss differences in opinions, bringing multiple views to strengthen your presentation. Presentations will be capped at 10 minutes (strictly enforced).
Assignment 3: Documentary Comparison Written Reflection:
In addition to presenting your chosen documentary, each student is additionally required to write a reflection on one video chosen by another pair. This assignment, which should be approximately 1500 words, should be a critical viewing of a video presentation. For this assignment choose at least two documentaries and compare and contrast their presentation styles, the hypotheses put forward (if any) and what evidence is used to support the main points. Importantly, use what you have learned in class to assess the quality, biases and kinds of science presented within the documentary. What was included, and as critically, what was omitted? Why do you think these choices were made? Lastly, did it change your views?
For those who are not familiar with critical viewing the following resources may be of some help
Each student will write a 8-10 page (undergrad) or 14-16 page (graduate) term paper. Papers must be 1.5 spaced, and page limits are excluding references. The paper may be on any topic within coastal and estuarine ecology of the student’s choosing. I don’t want to make you write papers on topics you aren’t interested in, and I don’t want to read papers you were bored writing. For graduate students who are interested there is an opportunity to conduct guided independent research for a small number (n=<4) of students. Please see me if you are interested and I will outline the project. If done correctly this project will most likely result in a peer-reviewed publication and the production of such will be the end goal. This will require a more intense effort throughout the semester than the term paper
We will have the opportunity to talk with Dr. Marah Hardt who is the Chief Ocean Scientist at Future of Fish and an independent scientist and consultant. She is also the author of our text Sex and the Sea. Dr. Hardt has graciously agreed to talk to our class at the end of the semester about the themes that are present throughout her book. Thus the last two and a half weeks we will be reading her book. On the Friday before her talk (December 9th) each student must submit a question for Dr. Hardt. She and I will go through these and come up with common themes to discuss. Each student should be ready to participate and engage both Dr. Hardt as well as other members of the class on the 12th.
Code of Academic Integrity:
We expect all students to abide by the Graduate School of Arts and Sciences’ code of academic integrity (http://gsas.columbia.edu/content/academic-integrity-and-responsible-conduct-research) or the Columbia College’s code of academic integrity (https://www.college.columbia.edu/academics/academicintegrity). Breaches of the student code, such as cheating or plagiarism (taking credit for the work of others), will not be tolerated. Any violation of the student code will be referred to the Dean’s Office.
Title IX makes it clear that violence and harassment based on sex and gender are Civil Rights offenses subject to the same kinds of accountability and support applied to offenses against other protected categories such as race, national origin, etc. If you or someone you know has been harassed or assaulted, you can find the appropriate resources at http://sexualrespect.columbia.edu. We also provide accommodations for students with documented disabilities; if applicable, please check with Columbia Disabilities Services (https://health.columbia.edu/disability-services) to ensure we are notified.
Lastly, we want to maintain a respectful atmosphere where students are free to discuss topics in a safe and collegial atmosphere. We will be covering some potentially contentious topics: discussion is encouraged while disrespect is strictly unacceptable. Everyone in this class should feel comfortable to express an idea, even if the idea is not popularly held. We encourage intellectual controversy and believe it is how we learn best.
September 5th Labor Day, No Classes
September 7th Physical Properties of Water
September 12th Movement of Water (Tides & Currents)
September 14th Nutrient Cycling: Nitrogen
September 19th Nutrient Cycling: Phosphorus & Carbon
Documentary: Racing Extinction
September 21st Sediment Processes. N cycle lab due
September 26th Atmospheric Influences (Deposition & Disease)
Documentary: Death Beach
September 28th Habitat Overview: The Arctic
October 3rd Habitat Overview: Rocky Shore
October 5th Habitat Overview: Estuaries
Documentary: The Cove
October 10th Habitat Overview: Mangroves
October 12th Habitat Overview: Sea Grasses
Documentary: Chasing Ice
October 17th Trip to AMNH (for the questions click here)
October 19th Midterm
October 24th Habitat Overview: Microbial Ecology
October 26th Habitat Overview: Coral Reefs
Documentary: Mission Blue
October 31st Habitat Overview: Deep Sea
November 2nd Upland Connections Pokemon Lab data due
Documentary: The Last Ocean
November 7th University Holiday: Election Day
November 9th Lab group presentations
November 14th Influence of Freshwater Management
Documentary: The Mystery of Eels
November 16th Science and Policy: Fisheries
November 21st Science and Policy: Invasive Species
November 23rd Historical Ecology
November 28th Marine Conservation
Documentary: Before the Flood
November 30th Evolution in the Marine Realm
December 5th History of the Hudson River
December 7th Shifting Baselines and Traditional Ecological Knowledge
December 12th Dr. Marah J. Hardt: class discussion Sex in the Sea
Final Exam December 16th 9:00
Introduction to Physical Oceanography (Stewart), Chapter 3
m: Bennett, W. A., and Jon R. Burau. “Riders on the storm: selective tidal movements facilitate the spawning migration of threatened Delta Smelt in the San Francisco Estuary.” Estuaries and Coasts 38.3 (2015): 826-835.
w: Fulweiler, Robinson W., and Elise M. Heiss. “A decade of directly measured sediment N.” Oceanography 27.1 (2014): 184.
m: Zhang, Fan, et al. “Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges.” Proceedings of the National Academy of Sciences 112.14 (2015): 4381-4386.
w: Daly, Kendra L., et al. “Assessing the impacts of oil-associated marine snow formation and sedimentation during and after the Deepwater Horizon oil spill.” Anthropocene (2016).
m: Jickells, Tim, and C. Mark Moore. “The importance of atmospheric deposition for ocean productivity.” Annual Review of Ecology, Evolution, and Systematics 46 (2015): 481-501.
w: Trathan, Phil N., et al. “Pollution, habitat loss, fishing, and climate change as critical threats to penguins.” Conservation Biology 29.1 (2015): 31-41.
m: Pfister, Catherine A., et al. “Historical baselines and the future of shell calcification for a foundation species in a changing ocean.” Proc. R. Soc. B. Vol. 283. No. 1832. The Royal Society, 2016.
w: Wetz, Michael S., and David W. Yoskowitz. “An ‘extreme’ future for estuaries? Effects of extreme climatic events on estuarine water quality and ecology.” Marine pollution bulletin 69.1 (2013): 7-18.
m: Kelleway, Jeffrey J., et al. “Seventy years of continuous encroachment substantially increases ‘blue carbon’ capacity as mangroves replace intertidal salt marshes.” Global change biology 22.3 (2016): 1097-1109.
w: Moulton, Orissa M., et al. “Microbial associations with macrobiota in coastal ecosystems: patterns and implications for nitrogen cycling.” Frontiers in Ecology and the Environment 14.4 (2016): 200-208.
m: Drew, Joshua. “The role of natural history institutions and bioinformatics in conservation biology.” Conservation Biology 25.6 (2011): 1250-1252.
w: STUDY FOR MIDTERM
m: Fuhrman, Jed A., Jacob A. Cram, and David M. Needham. “Marine microbial community dynamics and their ecological interpretation.” Nature Reviews Microbiology 13.3 (2015): 133-146.
w: Drew, Joshua A., Kathryn L. Amatangelo, and Ruth A. Hufbauer. “Quantifying the Human Impacts on Papua New Guinea Reef Fish Communities across Space and Time.” PloS one 10.10 (2015): e0140682.
m: Amon, Diva J., et al. “The discovery of a natural whale fall in the Antarctic deep sea.” Deep Sea Research Part II: Topical Studies in Oceanography 92 (2013): 87-96.
w: Fox, Caroline Hazel, Paul Charles Paquet, and Thomas Edward Reimchen. “Novel species interactions: American black bears respond to Pacific herring spawn.” BMC ecology 15.1 (2015): 1.
m: University Holiday: Election Day
m: Januchowski‐Hartley, Stephanie R., et al. “Future land use threats to range‐restricted fish species in the United States.” Diversity and Distributions (2016).
w: Arias, Adrian, et al. “Optimizing enforcement and compliance in offshore marine protected areas: a case study from Cocos Island, Costa Rica.” Oryx 50.01 (2016): 18-26.
m: Albins, Mark A. “Invasive Pacific lionfish Pterois volitans reduce abundance and species richness of native Bahamian coral-reef fishes.” Marine Ecology Progress Series 522 (2015): 231-243
w: Drew et al. Collateral damage to marine and terrestrial ecosystems from Yankee whaling during the 19th century. Ecology and Evolution (2016) Online Early
m: Lawson, Julia M., et al. Sympathy for the devil: a conservation strategy for devil and manta rays. No. e1731v1. PeerJ PrePrints, 2016.
w: Coleman, Richard R., et al. “Regal phylogeography: Range-wide survey of the marine angelfish Pygoplites diacanthus reveals evolutionary partitions between the Red Sea, Indian Ocean, and Pacific Ocean.” Molecular phylogenetics and evolution 100 (2016): 243-253.
m Pederson, Dee Cabaniss, et al. “Medieval Warming, Little Ice Age, and European impact on the environment during the last millennium in the lower Hudson Valley, New York, USA.” Quaternary Research 63.3 (2005): 238-249.
w: Sex in the Sea, Act 1&2
m: Sex in the Sea, Part 3
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