PCB 5443 ADVANCED ECOLOGY II: Communities and Ecosystems                             Spring 2018

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

Locations:       MMC GC 283B; BBC AC2 218

Go To Meeting 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

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

Date Topic Readings Textbook
  History, Energetics, Biogeochemical Cycles   (bolded = required)
9-11 Jan Course Overview & The Ecosystem Concept Tansley 1935; Odum 1969; Chapman et al. 2016 C1; W1
16-18 Jan Community Development & The Ecosystem Concept Connell and Slayter 1977; Bormann and Likens 1967
Ecosystem Energetics & Trophic Dynamics Lindeman 1942; Hairston et al. 1960 C10; W2-3
23-25 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; Follstad Shah et al. 2017 C7; W4
30-01 Feb Nitrogen and Phosphorus Cycles Schindler 1977; Slavik et al. 2004; Norby et al. 2010; Rosemond et al. 2015 C8-9, C14; W7-8
Exam 1
Meta-analysis & manuscript
Foundational Theories
13-15 Feb Niche & Neutral Theories Tilman 2004; Hubbell 2006; Fargione and Tilman 2005; Adler et al. 2007
Meta-analysis & manuscript
20-22 Feb Metabolic Theory of Ecology Brown et al. 2004
Meta-analysis & manuscript
27-01 March Consumer-Resource Interactions Tilman 1985; Hunter and Price 1992; Borer et al. 2014
Meta-analysis & manuscript
06-08 March Ecological Stoichiometry Hessen et al. 2013
Disturbance & Socio-Ecological Systems Grimm et al. 2017
Exam 2, Meta-analysis & manuscript
Integrating Communities & Ecosystems
20-22 March Biodiversity-Ecosystem Functioning Srivastava et al. 2009; Chase and Leibold 2002  C11
Meta-analysis & manuscript
27-29 March Predator Loss & Trophic Downgrading Schmitz et al. 2007
Ecosystem Resilience Scheffer and Carpenter 2003 C12
03-05 April Ecosystem Stability Ives and Carpenter 2007
Ecosystem Variance Dodds et al. 2012  W10-11
     Exam 3  
Spatiotemporal Scales & Predictions
10-12 April Ecosystem Modeling Bolker et al. 1998; Clark 2005
Meta-analysis & manuscript
17-19 April Ecosystem Connectivity & Landscapes Polis et al. 1997; Newman et al. 2017  C13
Meta-analysis & manuscript
24 April Final Exams Week Meta-analysis & Manuscript 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.

Student responsibilities: You are expected to do the assigned reading before class work and participate in class discussions throughout the term.  Each student is expected to participate in the meta-analysis, including extracting data, analyzing data trends, and developing a written section of a manuscript.

Grades: There will be three exams and a meta-analysis & manuscript. Your performance on these tests will account for 35% of your total grade. You must work with your classmates on a meta-analysis and write a section of a manuscript (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.

Meta-analysis & Manuscript. By the end of the first section of class, we will chose a topic for a group meta-analysis and manuscript. Students must participate in data gathering for the meta-analysis as well as write a section of the manuscript. Students will be evaluated on the quality and rigor of their work on the meta-analysis, as well as the clarity and conciseness of their writing of the manuscript section.  All students and Dr. Kominoski will be co-authors on the completed meta-analysis/manuscript (first-authorship and target journal will be discussed).

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.


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