Instructor: Dr Scott Creel 302 Lewis Hall, Phone: 994-7033. Email: screel@montana.edu
Office Hours: T 10-12, W 2-3. I am always happy to answer questions immediately after class, by email, or by appointment at other times.
Text: The
reading will
be a mix of journal articles with textbook chapters for background.
Required
reading (journal articles, book chapters) that does not come from the
textbook
will be linked from this web page (links in the syllabus below).
The
textbook is Conservation of Wildlife Populations,
by L.S. Mills
(Blackwell
Publishing, ISBN 1-4051-2146-7).
Graduate students:
We will use MATHCAD to
construct some
simple mathematical models of population dynamics, to model extinction
risk. You do not
need to know MATHCAD
ahead of time
to do these exercises. As much as possible, I want to focus on
the way that the models describe the population biology, rather
than the programming & syntax, but it is generally very useful to
master at least one programming application such as MATHCAD,
Mathematica, etc. The MATHCAD models of population dynamics
will be independent
study, parallel to in class lectures. MATHCAD is available
for free in the MSU student computer labs, and is installed on the
machines in Lewis 407. You can purchase a student license if you
want to run it on your own computer.
Undergraduates:
We'll use POPTOOLS, a free add-in to
MS Excel, to model extinction
risk. I am assuming that you have some basic experince with
Excel. If not, you should take some time during
the early part of
the semester to familiarize yourself.
Grading:
BIOL 447: Two in class exams (25%
each), a paper (20%), one take home test
(20%), homework (10%). The take home test will be to construct a
model to estimate a species'
extinction risk from demographic data, using Excel and POPTOOLS (Biol
447).
Course Outline:
We will cover some or
all of the following major
subjects, depending on time:
Human population growth - the 'arms race' between growth rates and carrying capacity
Extinction –
recent and historical rates
and causes of extinction and population decline.
Global warming and
its consequences for
ecology and conservation. This will focus primarily on
understanding the carbon cycle and atmospheric processes, how
anthropogenic influences are altering these, and the consequences for
ecological processes (mainly the distribution and abundance of
species). We'll address ecological economics to some extent
Speciation and the ESA – the process generating diversity, and tricky interactions between phylogeny, taxonomy and law.
Genetic issues in
conservation – inbreeding, hybridization, and the use of
molecular genetic tools in conservation.
Extinction risk –
demography,
population dynamics, stochasticity and PVA
Predation and Harvesting
– population dynamics with interspecific interactions, discounting,
externalities, publicly held goods
Community-level
approaches – Diversity and Stability
Landscape approaches – hotspots, gap analysis
These fall into five main sections: general issues, human impacts, genetic and evolutionary approaches, single-species approaches, and multi-species or location-based approaches.
Research Paper Instructions
(Updated on 10 September: Note that the instructions differ for BIOL 447 and 521. Also, the paper is 20% of the total score in BIOL 447, 15% in BIOL 521.)Cohen 1995.
Population growth and the
earth's carrying capacity. Science 269: 341-346. pdf
Optional paper (only 2
pages):
Haub, C. 2002. How many
people have ever lived on earth? Population Today, Nov/Dec
2003. pdf
This paper estimates (with much uncertainty) that 6% of all people ever
born are alive now.
Topic 4
CWP CH 3
Species and The Endangered Species Act. pdf
Rocky Mountain Wolves: Earthjustice vs USFWS. pdf
This case is currently being decided (unresolved as of 9/22/09)
Topic 5
Hybridization
Hedrick PW 2001. Conservation genetics: where are we now?
Trends Ecol. Evol.
11: 629-636. pdf
Allendorf et al.
2001. The problems with
hybrids: setting conservation guidelines. Trends Ecol Evol.
16:613-622. pdf
Hybridization
– including red wolf case study
CWP CH 9
F
- statististics
Keller
& Waller 2002. Inbreeding effects in wild
populations. Trends Ecol Evol 17: 230-241.
Inbreeding – cheetah
case study
Caro &
Laurensen 1994. Ecological and genetic factors in
conservation: a cautionary tale. Science 263:485-486.
Homework:
inbreeding coefficients and F statistics (DUE Friday 10/23 in class)
Topic 7
CWP CH 4,5,6
PVA and extinction
risk in small populations
Population
viability analysis - introduction
BIOL
521:Computer
Lab: MathCAD
tutorial, Introduction_Chapter6.MCD
"Getting Started"
Tutorials are in the help menu
in MathCAD. (The "Quicksheets" are also useful when looking at
specific questions once you know the software a bit.)
Introduction to ecological modelling in MathCAD is
here.
A
simple count based PVA in Excel. You will need to
download and install POPTOOLS
to run this
spreadsheet and most of the other Excel spreadhseets posted here.
Poptools is an interesting add-in for Excel that
provides menu-driven tools for many common demographic analyses (such
as the Leslie Matrix projections we will be
starting next week). It has good tutorials.
BIOL
521: A count based PVA in MatchCAD: PVA_Chapter17.MCD
- work through this exercise by writing the code yourself,
checking them as you go, if necessary, with the key.
Notes
to correct a simple but important logical error in Sinclair,
Fryxell & Caughley's key for the model of stochastic exponential
growth in PVA_Chapter17. MCD.
BIOL 521: Computer lab:
Biol
580 D-D PVA.xmcd - work through this exercise, which adds
density-dependence to the simple count based PVA model, by following
the provided code. I've also posted the worksheet as an mcd
file here. (If the XML file won't open).
PVA
– population growth models & Leslie matrix
projection of population growth
Populus has a good
module on age-structured growth
(under Single species dynamics). With three tabs at the
bottom, you can edit a life table, view the changes in the llife cycle
diagram and in the Leslie matrix. To the right you can plot the
associated lx curves, mx curves, age distributions, etc. A good
learning tool to soldify your grasp on the ways that a life table and a
Leslie matrix incorporate the information from a life cycle diagram.
Gotelli 1995.
Age-structured population
growth, pp. 56-71, In: A primer of ecology. Sinauer,
Leslie
calculator - a tool to understand age-structure growth This
is a GREAT tool to understand stable age distributions. Project for
several time steps with no changes to the Leslie matrix. Then
modify the Leslie matrix and repeat
the exercise.
BIOL
447: Example
Excel spreadsheet using POPTOOLS to analyze demographic data from
African wild dogs. There are two spreadsheets in this workbook
that you need to look at: one (labelled 'Elasticity and Sensitivity)
with the basic analyses of the Leslie
Matrix (r, R0, lambda, stable age distribution), elasticity and
sensitivity, and one (labelled 'Monte Carlo') with the stochastic
population projection.
BIOL 521: Computer
Lab: Leslie Matrix CH 14. Work
through this tutorial by writing the required code and checking with
the
key. Try to write the appropriate code for each
numberd step before
looking it up in the key, but use the key to understand and correct any
errors before moving to the next step.
BIOL 521: Computer Lab: BIOL 580 basic demography.MCD Work through this with understanding, just playing with the code as needed to test your understanding as you go. By the finish you should have all the tools to do a simple demographic PVA based on stochastic Leslie projections.
Brook, BW et al. 2000. Predictive accuracy of population
viability analysis in conservation biology. Nature 404: 385-387. pdf
Coulson et al. 2001. The use and abuse of population
viability analysis. Trends. Ecol. Evol. 16:219-221. pdf
EXAM
2 - Take home. Passed out November 18th. Due in class
November 23rd. I prefer that you turn in a paper copy and a copy
of your file(s) on a CD.
You
must work individually on the take home test!
BIOL
447 version NOTE: Do not use the
'convert life table to leslie matrix' tool in POPTOOLS.
BIOL 521 version as mcd
file
Topic 8
Harvesting
& sustainable offtake
part 1
CWP CH 8, 14
Ludwig 2001. Can
we exploit
sustainably? Pp 16-38 in Reynolds, Mace, Redford & Robinson
(eds) Conservation of Exploited Species.
Harvesting
& sustainable offtake part 2
Harvest
economics: stocks and discounting.
BIOL
521: Computer Lab: SFC Chapter
19 Tutorial and the brief handout
for this lab.
Brashares J, et al.
2004. Bushmeat hunting, wildlife declines
and fish supply in West Africa. Science
306: 1180-1183.
Topic 10
Community Ecology – diversity
and stability at population and community levels
More
notes on diversity & stability
CWP: CH 10
Tilman 1996.
Biodiversity: population vs. ecosystem stability. Ecology
77:350-363.
Community Ecology –
interactions among species and
consequences of species loss
Berlow 1999.
Strong effects of weak interactions
in ecological communities. Nature 398:330-334.
Habitat
Fragmentation and
Gotelli 1995.
Island Biogeography. In:
A Primer of Ecology, chapter 7, pp 172-195., Sinauer,
Habitat
Fragmentation and
Topic 12
Landscape
Ecology – gap analysis, hotspots and coldspots
Dobson
et al. 1997. Geographic distribution of endangered species in
the
van
Jaarsveld et al. 1998. Biodiversity assessment and
conservation strategies. Science 279:2106-2108.
Landscape Ecology – gap
analysis for
Kiester
et al. 1996. Conservation prioritization using GAP
data. Conservation Biology 10:1332-1342
Worm et al. 2005. Global patterns of predator diversity in
the open oceans. Science 309: 1365-1369.
EXAM
3 - final exam is on Monday Dec 14th 8:00-9:50 AM in the
regular Linfield Hall room.