SYLLABUS -- Population
modeling for conservation
Biology 596 Spring 2005
Prerequisites: Math 121 (or 122); Bio 354
and/or consent of lecturer
Professor: Helen Regan
Lecture: MW 09:00-9:50 LS 134 Office: PS 255-257
Lab: F 13:00-15:40 LS126 Office Phone: 594 2738
Office hours: M 14:00-15.00; W 14.00-15.00
or by appointment
Email: hregan@sciences.sdsu.edu
CONTACTING ME: See or call me during
office hours or by appointment. Email me. Leave me messages.
COURSE
DESCRIPTION AND OBJECTIVES
The aim of this course is to become familiar with the major
concepts and models in population ecology, and to learn and
use tools to solve applied problems in the conservation and management of
animal and plant populations.
Through the lectures, readings and computer labs you will
gain experience in applying concepts and using analytical methods to help
understand the dynamics of populations and help manage animal and plant
populations.
The following specific topics will be addressed:
The learning objectives of this course are for students to
be able to:
COURSE
MATERIALS
REQUIRED TEXTS AND READINGS
·
A lab notebook (loose leaf binder, spiral, or bound) will
be needed for the labs. A blank floppy disk (PC), and a hand calculator (or
working knowledge of Excel) will be useful in the lab.
·
Akçakaya, HR, Burgman, MA, and Ginzburg, LR. 1999. Applied
Population Ecology, Sinauer Associates. REQUIRED. This may be purchased
second hand from the Aztec bookstore or online from Web of Science http://ramas.com/apppopn.htm
·
Two EcoBeaker labs: “An Owl’s Life” and “Sick Fish”. REQUIRED.
·
There are additional readings available via Course Reserves
in the library (electronic and hard copy). A list of these appears at the
end of this document. Ten of these are available electronically; all are
available as hard copy. Some papers will be posted on Blackboard – I will let
you know as the course progresses.
GROUND
RULES
Attend class. Participate.
Ask questions. Be on time. Absolutely no food or drink in the lab. No late assignments will be
accepted. No make up exams given. Missing an exam will only be
excused in case of emergency with appropriate documentation (a note from a
health provider, etc.). Cheating is rarely an issue in ecology, however, please
note that University regulations concerning plagiarism and cheating (see
General Catalog) will be strictly enforced.
Keep on top of the course material by:
• attending lectures and labs (people who do not regularly
attend lectures and labs usually fail university courses)
• revising lecture notes;
• reading the required text;
• reading articles and chapters in the extra reading list
(on reserve in the library);
• working through examples;
• completing the labs each week;
• formulating your own questions;
• form a study group.
It is your responsibility to keep up to date with the
lectures and labs.
|
Assignment |
Percent
of total grade |
|
Exam 1 |
10% |
|
Exam 2 |
10% |
|
Exam 3 |
10% |
|
Assignment
1 |
15% |
|
Assignment
2 |
15% |
|
Assignment
3 |
35% |
|
Class
participation |
5% |
You will also be required to write up informal lab reports in the lab class. These should be shown to me (so I can check your progress) at the end of the lab class. They will not be graded unless they form an assignment (see above).
Grading
scheme: 90-100% (A); 80-90% (A-); 70-80% (B); 60-70% (C); 50-60% (D); <50%
(F = fail)
LECTURES: this course will consist of two
lectures per week. Lectures will emphasize main concepts from assigned reading,
illustrated with examples. Read assigned readings before class.
LAB: Labs are Fridays (13.00 – 15.40). Laboratory
exercises are primarily computer based. Most labs will be contained in the Applied
Population Ecology text and CD (or downloadable software from Web of
Science http://ramas.com/apppopn.htm. The
entire chapter (or supplementary reading) describing the assigned lab exercise
should be read before the lab on Friday. Bring the book to lab with you.
While students can work in groups, reports and assignments should be written
independently. If it’s more convenient for you, you may bring your own laptop
to the lab.
EXAMS: There will be three exams. All exams will be 2 hours.
They will cover the assigned reading and material covered in the lectures. They
will consist of short answer questions, calculations and longer essay type
questions. You will need to bring a calculator for each exam.
Assignments will be handed out in the lab and
are DUE 2 WEEKS AFTER THEY ARE FIRST ASSIGNED on the second Friday by 12pm.
COURSE
CALENDAR
|
Week |
Topic |
Text Reading (Applied Population
Ecology) |
Supplementary reading |
Assignments |
|
1 |
Intro; Simple population
growth Lab: Pop growth |
Chapter 1 |
SR1, SR3(sect 2.1) |
|
|
2 |
Density dependence:
continuous growth Lab: continuous density
dependence |
Chapter 3 |
SR2, SR4, SR5 |
Assignment 1 issued |
|
3 |
Density dependence:
discrete equations Lab: discrete density
dependence |
Chapter 3 |
|
|
|
4 |
Variation and
Uncertainty: sources Modeling demographic
stochasticity Lab: variation and
uncertainty |
Chapter 2 |
SR6 |
Assignment 1 due |
|
5 |
Variation and uncertainty:
modeling environmental stochasticity Revision: Q&A EXAM 1 |
Chapter 2 |
|
|
|
6 |
Age structure: Leslie
matrices Stochasticity Lab: age structured
models |
Chapter 4 |
SR7, SR3 (2.2 up to page
32) |
|
|
7 |
Age/stage structure,
life tables Sensitivity analysis Lab: stage structured
models |
Chapter 5 |
|
Assignment 2 issued |
|
8 |
Metapopulations and
spatial structure Lab: metapopulation
modeling |
Chapter 6 |
SR8 |
|
|
9 |
Metapopulations
continued Lab: case studies |
Chapter 6 |
|
Assignment 2 due |
|
10 |
Revision: Q&A EXAM 2 |
|
|
|
|
11 |
Population viability
analysis Lab: population
viability analysis |
Chapter 7 |
SR9, SR10, SR11 |
|
|
12 |
PVA: case studies Lab: PVA case study |
|
SR12, SR13, SR14 |
Assignment 3 issued |
|
13 |
Decision theory for
conservation Lab: decision theory
case studies |
|
|
|
|
14 |
Species interactions -
Predator-prey Species interactions -
epidemiology Lab: sick fish |
|
SR15, SR16, SR17 |
|
|
15 |
Course summary and
revision |
|
|
Assignment 3 due |
SUPPLEMENTARY READING LIST
Gotelli, N.J. Chapter 1: Exponential population growth, pp.
1-26. A primer of ecology. Sinauer, Sunderland, MA, 1995. SR1
Gotelli, N.J. Chapter 2: Logistic population growth, pp.
27-54. A primer of ecology. Sinauer, Sunderland, MA, 1995. SR2
Hastings, A. Chapter 2: Density independent population
growth, pp. 9-15, in Population Biology: concepts and models. Springer, NY,
1997. SR3
Mills M.G.L. and M.L. Gorman. Factors affeccting the density
and distribution of wild dogs in the Kruger National Park. Conservation Biology
11(6):1397-1406, 1997. SR4
Cohen, J.E. Population growth and earth’s human carrying
capacity. Science. 269(5222):341-46, July 21, 1995. SR5
Regan H.M., M. Colyvan, and M.A. Burgman. A taxonomy and
treatment of uncertainty in ecology and conservation biology. Ecological
Applications, 12(2):618-628, 2002. SR6
Crouse, D.T., L.B. Crowder, and H. Caswell. A stage based
population model for loggerhead sea turtles and implications for conservation.
Ecology 68(5):1412-23, 1987. SR7
Crone E., D. Doak and J. Pokki. Ecological influences on the
dynamics of a field vole metapopulation. Ecology 82:831-43, 2001. SR8
Shaffer, M.L. Population Viability Analysis. Conservation
Biology, 4(1):39-40. 1990. SR9
Boyce, M.S. Population Viability Analysis. Annual Review of
Ecology and Systematics, 23:481-506, 1992.
SR10
Doak D.F., P. Karieva, and B. Klepetka. Modeling population
viability of the desert tortoise in the western Mojave desert. Ecological
Applications, 4:446-460, 1994. SR11
Menges, E.S. Population viability analyses in plants:
challenges and opportunities. TREE, 15(2):51-56, 2000. SR12
Lindenmayer, D.B., M.A. Burgman, H.R. Akcakaya, R.C. Lay,
and H.P. Possingham. A review of the generic computer programs ALEX,
RAMAS/space and VORTEX for modelling the viability of wildlife metapopulations.
Ecological Modelling 82:161-174, 1995. SR13
Brook, B.W., J.J. O’Grady, A.P. Chapman, M.A. Burgman, H.R.
Akcakaya, R. Frankham. Predictive accuracy of population viability analysis in
conservation biology. Nature, 404:385-387, 23 March 2000. SR14
Vandermeer, J.H. and D.E. Goldberg. Chapter 6: Predator-Prey
(Consumer-Resource) Interactions, pp. 177-195. In Population Ecology: First
Principles. Princeton University Press, 2003. SR15
McCallum, H. and A. Dobson. Detecting disease and parasite
threats to endangered species and ecosystems. Trends in Ecology and Evolution,
10:190-194. SR16
Williams, E.S., T. Yuill, M. Artois, J. Fischer and S.A.
Haigh. Emerging infectious diseases in wildlife. Rev. sci. tech. Off. Int.
Epiz. 21(1):139-157, 2002. SR17