PCB 5443 ADVANCED ECOLOGY: Communities and Ecosystems                                     Spring 2017

Times:             Tuesdays MMC: 8:00-10:30AM; Thursdays BBC: 8:00-10:30AM

Locations:        MMC AHC-4 202; BBC MSB 112

Adobe Connect Remote Connection:

Instructor:        John Kominoski – office MMC OE 207; 305-348-7117;


Chapin, F.S., P.A. Matson, and P.M. Vitousek. 2011. Principles of Terrestrial Ecosystem Ecology, 2nd Edition, Springer. ISBN 1441995048;

Weathers, K.C., D.L. Strayer, and G.E. Likens. 2013. Fundamentals of Ecosystem Science, Elsevier. ISBN 978-0-12-088774-3;

Optional:                                                                                                                                          Coleman, D.C. 2010. Big Ecology: The Emergence of Ecosystem Science. University of California Press. ISBN 978-0-520-26475-5

Golley, F.B. 1993. A History of the Ecosystem Concept: More Than The Sum of Its Parts, Yale University Press. ISBN 0300055463

Other student materials: You must bring a laptop computer or tablet to class with program R installed and functioning (see notes below).

Class webpage: I will use Dropbox to distribute documents. Course syllabus, reading list, and assignments can be found at

Date Topic Topical reading Text
  History, Energetics, Biogeochemical Cycles   (bolded = required)
10-12 Jan Course Overview & The Ecosystem Concept Tansley 1935; Odum 1969 C1; W1
17-19 Jan Community Development & The Ecosystem Concept Connell and Slayter 1977; Bormann and Likens 1967
Ecosystem Energetics & Trophic Dynamics Lindeman 1942; Hairston et al. 1960; Pace et al. 2004 C10; W2-3
24-26 Jan Carbon Cycle (Photosynthesis, GPP, NPP) Chapin et al. 2006; Fourqurean et al. 2012 C5-6; W5-6
Carbon Cycle (Decomposition) Manzoni and Porporato 2009; Woodward et al. 2012 C7; W4
31-02 Feb Nitrogen and Phosphorus Cycles Schindler 1977; Slavik et al. 2004; Ardón et al. 2013 C8-9; W7-8
Nitrogen and Phosphorus Cycles Mulholland et al. 2008; Norby et al. 2010; Mann et al. 2014 C14
Exam 1
Foundational Theories
07-09 Feb Niche & Neutral Theories Tilman 2004; Hubbell 2006
Niche & Neutral Theories Fargione and Tilman 2005; Adler et al. 2007
14-16 Feb Metabolic Theory of Ecology Brown et al. 2004 and forum papers


Metabolic Theory of Ecology Brown et al. 2004 and forum papers
21-23 Feb Consumer-Resource Interactions Tilman 1985; Hunter and Price 1992 BBC joins at MMC on Feb 21st
Consumer-Resource Interactions Borer et al. 2014  
28-02 March NO CLASS – Work on DDIGs
  NO CLASS – Work on DDIGs
07-09 March Ecological Stoichiometry Hessen et al. 2013
Ecological Stoichiometry Cross et al. 2015  
Exam 2  
Integrating Communities & Ecosystems  
21-23 March Biodiversity-Ecosystem Functioning


Srivastava et al. 2009 C11
Biodiversity-Ecosystem Functioning Chase and Leibold 2002; Gamfeldt et al. 2008
28-30 March Predator Loss & Trophic Downgrading Bruno et al. 2005; Schmitz et al. 2007
Ecosystem Resilience Scheffer and Carpenter 2003; Folke et al. 2004 C12
04-06 April Ecosystem Stability Ives and Carpenter 2007
Ecosystem Variance Peters et al. 2004; Dodds et al. 2012 W10-11
Exam 3 NSF DDIG Proposal Draft 1 Due
Spatiotemporal Scales & Predictions
11-13 April Ecosystem Modeling Bolker et al. 1998 Download R and RStudio
Ecosystem Modeling Clark 2005
18-20 April Ecosystem Connectivity & Landscapes Polis et al. 1997
Ecosystem Services Daily and Matson 2008 C13
25-27 April Final Exams Week NSF DDIG Proposal Draft 2 Due  

Class Notes

Purpose: Provide a common foundation of the history, concepts, theories, and applications of community and ecosystem science for graduate students training to be ecologists. Each class will address a different concept or theory. Two textbooks will be used to provide background material for lectures and discussions of current papers from the primary literature. You may also benefit by access to a general ecology textbook as a reference for things you may have forgotten from your undergraduate classes, as well as the two optional textbooks on historical and modern foundations in ecosystem ecology. Students must familiarize themselves with basic graphing and analyses of community and ecosystem data in program R.

Pedagogy: Classes will contain a balance of lecture and discussion. Class time is used for answering student questions, discussions of the material, and review of core topics. Students will be required to graph, analyze, and interpret ecosystem data on exams. Students will be required to develop a NSF Doctoral Dissertation Improvement Grant (DDIG) proposal.

Student responsibilities: You are expected to do the assigned reading before class work and participate in class discussions throughout the term.

Grades: There will be three exams and two drafts of a NSF DDIG proposal. Your performance on these tests will account for 35% of your final grade. You must complete two drafts of a NSF DDIG and provide anonymous peer review of two first-draft proposals of fellow classmates during the semester (combined 35% of the total points). Finally, 30% of your grade will be derived from your participation in readings and class discussions. 

Exams. Exams will consistent of 3-4 essay questions associated with various topics from textbooks and primary literature discussed in class. Students will be required to graph, analyze, and interpret data in order to answer some questions. Exams will be given and completed outside of class. Completed exams are due by 5PM EST/EDT the date of the exam. Exams are closed book.

Proposals. NSF DDIG proposals will be evaluated for novelty, tractability, clarity, and concreteness. Evaluations will address the standard NSF criteria (Intellectual Merit, Broader Impacts). Students will also be evaluated on the quality and thoughtfulness of the feedback they provide in anonymous peer reviews of first-draft proposals.

Participation. Attendance in class in required and essential to obtaining a high grade. Students who miss class must submit to the Dropbox folder a paragraph summary of discussion points for each paper discussed in class on the day that the student was absent.

Computing: Download the free computer program R at: and RStudio at: You will be required to work with community and ecosystem data (your own or publically available) that you use to help develop your NSF DDIG proposal.


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