Instructor: Dr Scott Creel 302 Lewis Hall, Phone: 994-7033. Email: screel@montana.edu
Office Hours: TH 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). We are using the first edition (a second
edition is advertised but not available yet, so don't
accidentally order it).
Software:
Graduate students: We will use R to construct some simple
mathematical models of population dynamics, to model extinction
risk. As much as
possible, I want to focus on the population biology, rather than
the programming & syntax, but it is also generally
useful to become familiar with R,
because it is widely used for statistical analysis and
mathematical modelling in ecology. The R
models of population dynamics will be independent study, parallel
to in class lectures. R
is installed in the MSU student computer labs (Reid Hall,
Roberts Hall) and on the machines in Lewis 407. If you
want to run it on your own machine, you can download it from the
Comprehensive R Archive Network, CRAN. If you do
not already know R from
statistics classes at MSU, you should make yourself familiar
with the basics of R by
looking at "An Introduction to R", under the manuals link at the
CRAN site. Do this before we get to the section of
the course on demography and population dynamics. There are also
many good books available, such as Zuur, Ieno & Meester's "A
beginner's guide to R". "The R Book", by Crawley is
a comprehensive manual, well worth the investment for a new
graduate student.
Undergraduates: We'll use MS Excel, to model extinction risk. I am assuming that you have some basic experience with Excel. If not, you should take some time during the early part of the semester to familiarize yourself with entering data, using formulas, copying and pasting in a way that maintains correct cell references (that is, understanding the use of "$" in cell references), and making graphs.
For demography
and PVA, POPULUS has a nice module to supplement the
book. Download here
and follow the installation instructions. Populus is a
menu-driven program that shows graphical output from common
models in population biology, from Don Alstad at the University
of Minnesota.
Grading:
BIOE 440: Two in class exams
(25% each, one in finals week), a paper (20%), one take home
test (15%), and an in class debate (15%). The take home
test will be to construct a model to estimate a species'
extinction risk from demographic data, using Excel and POPTOOLS.
Research Paper Instructions Note that the instructions differ for BIOE 440 and 521. Although the paper is not due until later in the semester, you should pick a topic and begin looking for articles with plenty of lead time.
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.
Cohen 1995.
Population growth and the earth's carrying capacity.
Science 269: 341-346. pdf
(optional reading) Arrow et al 1995. Economic
growth, carrying capacity and the environment. Science
268: 520-521 pdf
Topic 4
CWP CH 3
Species and The Endangered Species Act. pdf
DPS
policy from Federal Register
O'Brien &
Mayr Bureaucratic mischief: recognizing endangered species and
subspecies. Science 251:1187-1189 pdf
Identifying
a
DPS/ESU in practice - Waples, Moritz, Crandall
Topic 5
Hybridization
Hedrick PW 2001. Conservation genetics: where are we now?
Trends Ecol. Evol. 11: 629-636. pdf
(optional
reading)
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
Topic 7
CWP CH 4,5,6
PVA and
extinction risk in small populations
Population
viability
analysis - introduction
BIOL
521:Computer Lab: Review "An Introduction to R" under
the manuals link at CRAN
BIOL 521: A
simple count based PVA - exponential and
density-dependent population growth models with stochasticity
for Yellowstone grizzly bear data.
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.
Leslie
calculator
- a tool to understand deterministic 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.
Basic Leslie matrix Excel spreadsheet - understanding
deterministic population projections. Another tool to understand Leslie
projections, using a simple spreadsheet approach to
implement the projections. Allows you to fiddle with adding a
harvest, but you can ignore that for now.
BIOL 447: Example EXCEL
spreadsheet using stochastic Leslie matrix projection to
determine the probability of pseudo-extinction.
This implements the projection in two ways, to illustrate good
and less-good methods. There is a pop-up set of notes
that explains the functions and formulas that accomplish the
necessary steps.
BIOL 521: Computer
Lab:
Stochastic Leslie matrix projection v1:
This lab uses the popbio package to
implement stochastic projection and estimate
extinction risk via the 'multiple matrixes' approach.
That is, at each time step, it resamples from a set of
projection matrices (each matrix comes from a single year of
observation).
BIOL 521: Computer
Lab:
Stochastic Leslie matrix projection v2:
This lab uses the popbio package to implement stochastic
projection and by treating the entries in the projection
matrix as variables with a defined distribution, mean and
variance.
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. You must work individually on
the take home test. Passed out WED 11/28, due FRI
11/30.
BIOL
447 version
BIOL
521 version
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.
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 Thursday Dec 13th
6:00 PM in the regular room (Cheever 213).
The final will cover all of the topics relared to genetic
approaches, and the material we cover in the last two weeks,
after PVA.