Class Hours & Location: MWF
Cheever Hall, Room 213
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).
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.
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
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. BIOE 521:
BIOE 521: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 R. The paper has extra requirements for graduate students (details below).
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.
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
– methods of
measurement, broad patterns, and processes that maintain
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.
CWP = Mills, Conservation of
CWP = Mills, Conservation of Wildlife Populations.
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
CWP CH 3
Species and The Endangered Species Act. pdf
policy from Federal Register
Mayr Bureaucratic mischief: recognizing endangered species and
subspecies. Science 251:1187-1189 pdf
DPS/ESU in practice - Waples, Moritz, Crandall
Allendorf et al. 2001. The problems with hybrids: setting conservation guidelines. Trends Ecol Evol. 16:613-622. pdf
CWP CH 9
F - statististics
Keller & Waller 2002. Inbreeding effects in wild populations. Trends Ecol Evol 17: 230-241.
Inbreeding – cheetah case study
& Laurensen 1994. Ecological and genetic factors
in conservation: a cautionary tale. Science 263:485-486.
CWP CH 4,5,6
extinction risk in small populations
analysis - introduction
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.
error and apparent density dependence - Excel
spreadsheet illustrating the 'induced correlation' between
population growth rate and N when one samples
from a normal distribution of N (as opposed to a normal
distribution of growth rates). Illustrates why sampling
error in estimates of population size produces a pattern that
looks exactly like density dependent population
CWP CH 7
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
- 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
BIOL 521: Computer
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
BIOL 521: Computer
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
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
CWP CH 8, 14
Ludwig 2001. Can we exploit sustainably? Pp 16-38 in Reynolds, Mace, Redford & Robinson (eds) Conservation of Exploited Species.
Brashares J, et
al. 2004. Bushmeat hunting, wildlife declines and fish
supply in West Africa. Science
stability at population and community levels
on diversity & stability
CWP: CH 10
Community Ecology – interactions among species and consequences of species lossNotes on'weak interaction' effect in diversity-stability relationship.
1995. Island Biogeography. In: A Primer of Ecology,
chapter 7, pp 172-195., Sinauer,
Watling JI & Donelly, AI 2006. Fragments as islands: a synthesis of faunal responses to habitat patchiness. Conservation Biology 20:1016-1025.
al. 1997. Geographic distribution of endangered
species in the
al. 1998. Biodiversity assessment and conservation
strategies. Science 279:2106-2108.
Landscape Ecology – gap analysis for
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,