ABIO564

Course Objectives:

General. Course requirements in Ecology and Evolutionary Biology (EEB), at both the master's and doctoral level, include enrollment in BIO 564, Integrative Principles of Ecology. This course contributes to rigorous preparation for the Qualifying Examination, Part I (QE I) in Ecology and Evolutionary Biology. The EEB faculty maintains a list of questions from which the QE I is composed. Collectively, the listed questions span topics from across Population Biology, as well as some ancillary issues. The Spring 2012 version of BIO 564 will focus on conceptual prinicples that integrate understanding in Population and Community Ecology. Acquisition of these concepts should prepare students for most QE I questions addressing Ecology. BIO 563, ordinarily offered during Fall semester, should prepare students for QE I questions concerning Evolutionary Biology.

Specific. Formulation of a scientifically sound research project in Ecology - i.e., a study likely to make a visible contribution to the discipline - begins with an understanding of Ecology's theoretical foundations. This course addresses the conceptual framework of contemporary Ecology, a set of quantitative principles guiding our integrative, predictive understanding of the complexity observed across both natural and managed landscapes, and for constructing scientific analyses of applied problems. The course therefore focuses on the core of this framework, a series of well-defined mathematical models for the dynamics of single populations, and for the growth of ecologically interacting species.

Understanding the integrative principles of Ecology requires familiarity with derivatives, integrals, differential and difference equations; scan any graduate text used in competitive EEB programs. Links to various levels of (undergrad) math review can be found on The Calculus Page.

Visualization can accelerate some students' understanding of population dynamics. NSF has funded devlopment of free software, Populus, that includes the majority of models to be discussed in class. The software further allows exploration of a number of other topics beyond the BIO 564 syllabus. You may wish to download Populus.

... despite the field's reputation as a soft science, nearly all of biology is now ripe for quantitative analysis ...
Phillips, R., Quake, S., Physics Today, May 2006.

Course Procedures:

Each unit will begin with a lecture, or lectures, pertinent to the topic. Presentation will emphasize mathematical models from which ecologists deduce integrative principles. For most topics, the instructor will demonstrate model predictions by solving quantitative problems. For some topics, the class will discuss papers reporting empirical tests of model predictions. Toward the end of the semster, time permitting, the class will collect the topics addressed, and answer questions of the sort that can appear on the EEB QE I.

Student assignments will be linked to this page (see below). Discussion in class will assume that students have read material provided before the associated class meeting.

Text:

No textbook is required. Luckily for you, Rob J. de Boer hs provided a free electronic copy of his 2006 text, Modeling Population Dynamics: a Graphical Approach, which we can use as needed.

Grade Determination:

Course grades will depend on [1] results an exam administered near the end of the semster, [2] the quality of three, graded problem sets, and on [3] a critique of an assigned paper from the recent literature. The exam and the problem sets will emphasize mathematical methods required to understand both essential concepts and tests of hypotheses in Ecology. Students may, if they wish, work on problem sets as a group. Each student will be assigned a different paper for critique. The Exam/Problem Sets/Critique will be weighed as 40/30/30 in calculating final grades.

You can view possible test questions (pdf).

Each student will write an anlaysis/critique of a separate ecological publication. The paper should be approximately 8 pages (double-spaced) in length. Grading of the crtique will depend on the understanding of general ecological principles conveyed by the paper. Each student will select his/her particular paper from a list of recent publications (pdf).

A graduate student working toward an advanced degree in Ecology and Evolutionary Biology should achieve a level of proficiency in these assignments matching, or exceeding, levels reached by motivated undergraduates in BIO 320 (Ecology). Students working in other disciplines presumably will assess if this course suits their intellectual interests or professional goals, and then act accordingly.

Whoever despises the high wisdom of mathematics nourishes himself on delusion.
da Vinci, 1489.

Unit Topic	Lectures
Overview of Ecology	Understanding, Prediction, Concepts
Density-Independent Dynamics	Environmental Stochastcity, Spatial Variation
Age, Stage Structure	Life Tables, Leslie Matrix
	Stable Age Distribution, Life Histories
Density-Dependent Dynamics	Self-Regulation, Predictability
	Demographic Stochasticity, Time-Delayed Feedback
Dynamic Overcompensation	Discrete Logistic, Ecological Chaos
Metapopulation Dynamics	Colonization-Extinction, Dispersal and Coherence
Inter-Specific Competition	Invasion, Exclusion, Coexistence
	Niche Overlap vs Self-Regulation
Consumer-Resource Dynamics	Predator & Prey, Herbivory
	Parasitism & Disease
Mutualism	Stability, Mosaic Coevolution
Indirect Interactions	Apparent Competition
Quantifying Species Diversity	Estimating Diversity, Abundance Models
	Species-Area Relationship, Geographic Gradients
Community Organzation	Biotic Structure versus Neutrality

Date	Type of Assignment	Link
19 January	Preview: BIO 320 Test Questions	pdf
26 January	Study Pp. 9 - 16 in de Boer (2006)	See "Text" above
26 January	Introduction	pdf
26 January	Density Independence I	pdf
26 January	Density Independence II: Stochasticity	pdf
2 February	Life Histories, Population Projection	pdf
9 February	Study Pp. 17 - 21 in de Boer (2006)	See "Text" above
9 February	Self-Regulation	pdf
9 February	Time-Delayed Logistic Growth	pdf
16 February	First Problem Set	pdf
16 February	Discrete Time Growth	pdf
16 February	Optional: Bifurcations and Chaos	pdf
16 February	Nonlinear Dynamics: Overcompensation	ppt
16 February	Overcompensation and Predictability	pdf

23 February	Interacting Species: Overview	pdf
23 February	Two-Species Competition: Niches	pdf
23 February	Lotka-Volterra Competition	pdf
23 February	Competition: Graphical Analysis	pdf
23 February	Two-Species Competition: Spatial Heterogeneity	pdf
23 February	Competition: Niche Displacement	pdf
23 February	Competition: Caveat	pdf
23 February	Read Pp. 79 - 83 in de Boer (2006)	See "Text" above

1 March	Consumer-Resource Dynamics: Overview	pdf
1 March	Predator-Prey Dynamics	pdf
1 March	Mutualism	pdf

8 March	Second Problem Set	pdf
8 March	Disease Ecology: SIR Epidemic	pdf
22 March	General Epidemic: Vaccination	ppt
22 March	Evolution of Pathogen Virulence	ppt

29 March	Species Diversity, Rank-Abundance Models	pdf
29 March	Species Area, Latitudinal Diversity Gradient	pdf

12 April	Stability, Diversity and Complexity	pdf
12 April	Niches and Neutrality I	pdf
12 April	Niches and Neutrality II	pdf

19 April	Third Problem Set	pdf
19 April	Indirect Interactions
19 April	ESA and "Earth Stewardship"	pptx

3 May	Exam

Last 4 of ID	Problem Set 1 (10)	Problem Set 2 (10)	Problem Set 3 (10)	Exam (40)	Critique (30)
0649	10	9.5	9.5	23	27
2096	9.0	9.0	9.0	27	22
2203	10	9.5	9.5	25	24
5416	9.0	9.5	8.5	25	22
7629	9.0	7.5	8.5	36	29
9072	10	9.0	9.5	22	22
9216	9.0	8.5	8.5	34	26
abcd	9.0	8.0	8.5	35	24
zyxw	8.0	9.0	7.5

Integrative Principles of Ecology ABIO 564 Spring 2012

Integrative Principles of Ecology
ABIO 564
Spring 2012