Main index page -- Population Ecology, ZOO 4400/5400, Spring 2013

Main hub. I suggest setting a bookmark to this page.  RELOAD/REFRESH FROM TIME TO TIME!!  
            Jump to web page navigation help note

Underlined text is generally hot linked (mostly blue; some blue text in internal pages is not underlined and not hot linked) 

        You will submit all homework electronically to:

2013: Most downloads should be done from WyoWeb course site

Jump to area for additional downloads (including links to movies of the discrete logistic for various r values

                                       McDonald home page

Lecture Notes

Go to Lecture 1 (14-Jan-13)      [Introduction to the course]
Go to Lecture 2 (16-Jan-13)      [Kaibab deer; the scientific method]
Go to Lecture 3 (18-Jan-13)      [Models, experiments, pseudoscience]

21-Jan-13 Martin Luther King Holiday
Go to Lecture 4 (23-Jan-13)      [How to learn, inflow, outflow, stability, introduction to exponential growth]
Go to Lecture 5 (25-Jan-13)      [Logistic growth, lags, patterns of variation in l (little r)]

Go to Lecture 6 (28-Jan-13)      [More on the logistic equation; Populations: definitions,
                                                               characteristics, processes, and limits]
Go to Lecture 7 (30-Jan-13)      [Dynamics of populations; Population estimation (web only)] 
Go to Lecture 8 (1-Feb-13)       [Intro. to demography, Type I-III survivorship curves, patterns of mortality, Simpson's paradox.]

Go to Lecture 9 (4-Feb-13)       [Patterns of survival and mortality, part 2]
Go to Lecture 10 (6-Feb-13)     [Sex ratios, Natality]
Go to Lecture 11 (8-Feb-13)     [Intro. to matrix population models]

Go to Lecture 12 (11-Feb-13)    [Matrix models (cont.). Formulation, age class vs. age, life cycle graph, outputs]
Go to Lecture 13  (13-Feb-13)   [Graphs and equations; note that in-class lecture will be different]

End of material for Exam 1       Exam 1 Friday 15-Feb-13

Go to Lecture 14 (18-Feb-13)    [Matrix models cont. Ferret matrix, approach to equilibrium] 
Go to Lecture 15 (20-Feb-13)    [Sage-Grouse case history -- stage-classified models]
Go to Lecture 16 (22-Feb-13)    [Adding stochasticity to matrix models -- stochastic population fluctuations]

Go to Lecture 17 (25-Feb-13)    [Intraspecific competition; discrete logistic, chaos -- deterministic population fluctuations]   
         Movies below apply to Lectures 16 & 17
         Go to movie of discrete logistic 2-cycle (r = 2.2) case   Go to movie of discrete logistic chaos (r = 3) case
                  Go to movie of discrete logistic converge-to-K (r = 1.5) case
Go to Lecture 18 (27-Feb-13)    [Discrete logistic -- initial conditions, experimentally induced chaos]
1-Mar-13   In-class questions, discussion and quiz

Go to Lecture 19 (4-Mar-13)    [Interspecific competition -- niche, character release, limiting similarity]
Go to Lecture 20 (6-Mar-13)    [Lotka-Volterra 2-spp. competition equations; isoclines; competitive coexistence]
Go to Lecture 21 (8-Mar-13)     [More on Lotka-Volterra trajectories]

Go to Lecture 22 (11-Mar-13)   [Intro. to predation; mesopredator ecological release; Bay-breasted Warbler functional & numeric response]
Go to Lecture 23 (13-Mar-13)   [Lotka-Volterra predator-prey cycles]

Spring Break 18-22-Mar-13

Go to Lecture 24 (25-Mar-13)    [Logistic prey growth; stable and unstable configurations]
Go to Lecture 25 (27-Mar-13)    [Harvest models]
29-Mar-13 No class (Easter break)

Go to Lecture 26 (1 and 3-Apr-13)    [Experimental and empirical studies of competition and predation]
End of material for Exam 2

Exam 2 Friday 5-Apr-13

Go to Lecture 27 (8-Apr-13)   In-class lecture on risk disturbance   [webnotes on Population regulation]
Go to Lecture 28 (8-Apr-13)     In-class on Population regulation and Turchin [Turchin et al. paper on lemmings as predators]
Go to Lecture 29  (10-Apr-13)     [Density-dependent vs. density-independent regulation -- graphical]
Go to Lecture 29 (continued)  (12-Apr-13)     [Density-dependent vs. density-independent regulation -- graphical]

Go to Lecture 30  (15-Apr-13)   [Population regulation -- empirical experimental case histories]
Go to Lecture 31  (17-Apr-13)   [Wrapup of population regulation. Infectious disease model]
Go to Lecture 32
  (19-Apr-13)   [Infectious disease model -- solving equations with too many unknowns by using known bounds]

Go to Lecture 33  (22-Apr-13)   [Infectious disease model -- graphical approaches; smooth or oscillatory convergence to I*]

Lectures beyond this point not yet updated for 2013

Powerpoints for the remaining lectures (and the corresponding assigned original papers in Nature or Science) will be available on the WyoWeb course file site

Go to Lecture 34  (24-Apr-13)  TBA  (this is an older population genetics lecture, which I may not cover this year)

3-May-13 possibly an in-class review of material since Exam 2. 

Final exam is WEDNESDAY 8-May-13 8:00 to 10:00 in BC 138 (our regular classroom)

I will try to post "nearly final" Powerpoints ahead of scheduled lectures.
I will often revise the Powerpoints after I give a lecture, so that it more closely reflects what I actually covered in class. 
Look for a "revised dd-mmm-yy" message so that you can tell whether anything you want to print out is the "latest version".

    Go to web page for Poisson distribution and patterns of dispersion (background for Homework # 2 and # 4)

Download Excel demo of time-step analysis   (HW4, trajectories for N1, N2, 1D map)

Go to web page for Poisson distribution and patterns of dispersion (items related to Homeworks # 2 and # 4)

Excel tutorials

Download Word doc. giving some tips for working with Excel     Download example Excel spreadsheet

Download demo. of Excel charting of X-Y data with linear regression

Other downloads

Go to glossary of terms used in matrix algebra      

Go to movie of discrete logistic 2-cycle (r = 2.2) case        Go to movie of discrete logistic chaos (r = 3) case

Go to movie of discrete logistic converge-to-K (r = 1.5) case

Unstable coexistence "movie"    Stable coexistence movie, Case 1    Stable coexistence Case 2

Download Excel demo of time-step analysis  

Download a Word document containing a few sample questions (and their answers) from Exam 1 '03

Go to Glossary of genetic terms       Go to worked FST calculation web page.

Go to Excel spreadsheet for calculating gene frequencies and local inbreeding coefficient from genotypic counts

Dr. David McDonald    BioSciences 415     766-3012

Office hours W 10:00-12:00, Th 2:30-3:30 or by appointment

TA:  Sara Decker                 BioSciences 441      

Office hours       MW 3-4 or by appointment

A note on navigating the web pages:

Figures, Equations and Required Readings are labeled in a "chapter-like" manner, with each lecture as the equivalent of a chapter.  That is, Lecture 1's web page will be "Chapter 1".  All Figures in that web page will be numbered Fig. 1.1, 1.2, ...1.n for the n Figures it includes.  The same will be true for Equations (numbers for which will be toward the right-hand margin).  I will try to hot link most references to Figures or Equations WITHIN a web page, but may not do so BETWEEN web pages.  That is, a reference to Eqn 1.1 in the 2nd web page ("Chapter 2") might require you to jot that number down and surf back later.  The hot links will be the standard underline format.  I will have links between all the web pages that I design for this course.  I may even put in some external links. Come see me if you need help on browsing the web pages.  Please let us know, also, if you find typos, pages that won't print properly, or other glitches.
Reading numbers may change if the lecture schedule shifts -- the updated list of number will be reposted occasionally both on the web and in the WyoWebs Readings folders.

Finding required readings:

You can download various required readings (in PDF format) and other files by going to WyoWeb.

1) Go to the WyoWeb page (by going to the UW home page and clicking the WyoWeb link)
2) Log in (your campus username and password)
3) Click the "Student" tab near the top of the page
4) Near the upper left of the resulting window you should see a box that says "My Courses."
Click on the blue words "For Spring 2013 courses, click here"
5) In the next page, the biggest area should be labeled "Courses I'm taking"
6) Hit the "Population Ecology" link
7) On the Population Ecology page, the box near the upper left will have a link called "Files."  Click that. 
8) That will bring up a window that has a list of subfolders.  Choices include "Powerpoints", “Required readings ” (set of required readings including those from the Gotelli text), “Suggested” (recommended, but not required) and “Handouts” (most of these will be given out as hard copies in class).  Click the subfolders (make the arrow/triangle go from pointing sideways to pointing down, otherwise you won't be able to see or access the files) then click the file links to download them.

Required readings are listed by Lecture number and date corresponding to when I cover that material in class, just before the ".pdf" extension.  The lecture number is equivalent to the Lecture number in the syllabus. 

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