BIOE 440R/521 Conservation Biology     

Class Hours & Location: MWF 12:00- 12:50,  Lewis Hall Room 306. 


Instructor: Dr Scott Creel 311-A Lewis Hall, Phone: 994-7033. Email:
TA:  Egil Droge, AJM Johnson Room 7 (in the basement). Email: Egil will conduct regular help sessions for the use of R and questions on class material on Thursday at 2:00 in the Ecology library, and is available to help with these at other times by appointment.

Undergrad TA: Noah Bosworth.   Email:  (best contact). Phone (207)-629-7649 (not preferred).  Noah will assist Egil at the help sessions and is available for help after 1:00 on Fridays and between 10:00 and 5:00 on Thursdays.

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 and textbook chapters. 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, 2nd edition by L.S. Mills  (Blackwell Publishing, ISBN 978-0-470-67149-8). 

We will use the free software package to analyze data and to construct  simple mathematical models of population dynamics to estimate extinction risk.  To conduct research in conservation biology and ecology it is now absolutely necessary to become proficient with R, which is very widely used for statistical analysis and mathematical modelling in ecology.    R is installed in the MSU student computer labs but I very strongly suggest that you download it (free) from the Comprehensive R Archive Network, CRAN.  We will use R within R Studio, a free interface that makes it easier to learn and use R.  The class will use a series of annotated examples, help sessions and homework to help you learn how to analyze ecological data and construct population models in R.

There will be reading assignments specific to the R software, from "A Beginner's Guide to R" by Zuur, Ieno and Meesters.  You can download a free copy of this book using MSU's SpringerLink connection, as long as you are logged onto an MSU-domain computer:   (click the 'download book' link to get the entire thing as a pdf).

One of the positive aspects of working with R is that there are many excellent sources of help. Some of these are:

  1. The Cookbook for R website is has a nice index of example scripts, with explanations, for all basic operations like importing data, manipulating it, making graphs, etc. This is a very useful resource for new users.
  2. The Quick-R website is similar to the cookbook. I prefer the cookbook site but they are both good.
  3. The R homepage has links to manuals, reference cards, webpages and user-groups. Authoritative, but not as user-friendly as the first two.
  4. For example code you can very often just use google, searching for something like “r change axis range”. Just include R and the thing you are trying to accomplish and you’ll often find a good example that solves your problem, with code provided.
  5. If google doesn't work, try and search the site with R included in your search term.
  6. For many types of statistical analysis, the UCLA statistical consulting department has truly excellent explanations with great example code.

The CRAN website also has links to many open-access books on R:


BIOE 440: Three in-class exams (10% each, one in finals week), a paper (15%), one take home test (15%), and ~8 homework assignments (40%).
BIOE 521: The same as 440, except that homework will count for only 25%, there is an in-class presentation in the final two weeks (15%) and there are different requirements for the paper and take home exam.

Research Paper Instructions  Due Wednesday November 16th   You should look at the requirements, pick a topic and begin looking for articles with plenty of lead time. 
Instructions for the citation format are here.  Using some sort of reference manager software saves a lot of time by allowing you to single-click download citations from sources like Google Scholar, and then use a single-click 'cite-while-you write' feature to cite any downloaded reference in your paper and have it added automatically to the paper's bibliography, in any format you choose. MSU has a free subscription to EndNote for students, click for details of how to download and use.

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

Biodiversity - methods of measurement, broad patterns, and processes that maintain diversity
- 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 Wildlife Populations, 2nd edition. 
ABGR = Zuur, Ieno & Meesters, A Beginner's Guide to R.

Subject Reading Homework: due dates will be announced in class when assigned

1 Conservation Biology & Human population growth - a race between N & K.

Utilitarian and Transcedentalist philosophies of conservation
1. CWP CH 1
2. Cohen 1995.  Population growth and the earth's human carrying capacity.  Science 269: 341-346. pdf  Also see figs 1 & 2 in Nekola et al. 2013 TREE 28:127-130 pdf
Balmford et al. 2002.  Economic reasons for conserving wild nature. Science 297: 950-953 . pdf   (not assigned reading, just background material for in class)


R: Exercise One
Data file used in Exercise One

R: Exercise Two  (data set for HW1 from US Census of 2010, as orginally formatted by US Census Bureau. Same data here as a txt file to read into R.

HW 1 due Wed 14th in class.
Look at R Exercise Two for examples that will allow you to do HW 1 using R

HW1  (word docx file), PDF here

Egil will have the help session this week on TUESDAY 3-5 in Lewis 306 (not in the Ecology Library) if  you need help with HW 1. 

Biodiversity: how many species, what patterns?  past and present extinction rates.

Just in time for the discussion of the number of species in 2016:  a new beaked whale species in the genus Berarduis. In 2015: the jellybean frog Noblella madreselva from the Andes and China's bonehouse wasp Deuteragenia ossarium2014's winner was the bat out of hell (Murina beelzebub). In 2013, a new carnivore species, the olinguito, was added.  Just after we discussed this in 2012, a new monkey species was discovered in DR Congo.  In 2010 it was the cowboy frog (Suriname), among others. In 2009 it was the Lesula monkey and the Yoda bat (New Guinea)...

Western black rhino goes extinct at the same time
1. CWP CH 13
2. Pimm et al. 1995.  The future of biodiversity.  Science 269: 347-350.  pdf
3. Mora et al. 2011.  How many species are there on earth and in the ocean?  PLoS Biology 9:1-8 e1001127 pdf

May 1988. How many species are there on earth? Science 241:1441-1449. (not assigned reading, just for background material in class).



Study Guide.  Only questions 1-5 in the guide will be covered on this exam.

The essay questions will be broad, show-what-you-know style questions.  The best answers will:
- be well organized and well written
- be clear and direct
- include supporting examples from class or the reading
- include verbal, graphical and algebraic explanations when possible.

Designing and interpreting studies

Case study - Distance sampling to estimate the population density of magpies and the factors affecting their distribution. This project will require you to develop a hypothesis, develop a sampling design appropriate to test it, collect and analyze the data.

BIOE 440R - magpies and/or crows. 

1. CWP CH 2
2. CWP CH 4
3. Christianson & Creel 2014. Ecosystem Scale Declines in Elk Recruitment and Population Growth with Wolf Colonization: A Before-After-Control-Impact Approach. Plos One 9(7): e102330
4. Chandler, R. 2014. Distance sampling analysis in unmarked. (pdf)

Elk counts and inferences: introduction to estimation of population size.


Leopard example

HW2A - OLS and GLM regression in R. DUE MONDAY 10/3 (ignore old date on the file)
Data sets for HW2A:  hwq1data    hwq2data

Remember that there is a menu option in R Studio to set the working directory:

1. Create a new R script to do the analysis: under the File tab on the top menu, select 'New File' then click  'R Script' on the pop-up menu.
2. Save your R script to the location where you put the datafiles when you downloaded them (for example, R script file and datafile both on the desktop).
3. Under the Session tab on the top menu in R Studio, select 'Set Working Directory' and click 'To Source File Location'. 
4.  Read a data file into R with a line of code such as:
data.for.q1 <- read.csv("hwq1data")

Alternatively, use the Import Dataset button in the top right window of R Studio, which allows you import a datafile directly from the web by pasting the URL from browser.

HW2B - hypothesis statement, sampling design and methods for magpie data collection.  DUE FRIDAY 10/7

HW3 - magpie data  Example data sheet
Copy of completed data

HW 4 - Detailed instructions for
magpie analysis 

After converting sighting angle to fall between 1 and 90 (see detailed instructions in pdf just above), you must convert the angle from degrees to radians before taking the sine.  An example using Excel, though this is also easy in R.

Some further explanation: how to deal with transects that had no animals detected
Example used in class

A short summary of regression

Optional: Regression Models tutorial with SWIRL.
R: Exercise Three
A  Hypothesis testing with simple and multiple regression
Data file: kenyaherdsize2.txt

R exercise Three B: Generalized Linear Models.

R: Exercise Three C Model selection and multimodel inference
Data file: kenyaherdsize3.txt

R: Exercise Four
Estimating population density with distance sampling

Data files:


Anthropogenic climate change:
1. Physical mechanisms: parts 1, 2, 3, 4

2. Ecological consequences
-- Primary: distribution, abundance, phenology
-- Secondary: change in community structure
       - new interspecific interactions,
       - different phenological changes at different trophic
        levels causing food web disruptions

NOAA - 800,000 year summary - Atmospheric CO2 record

NASA - global temperature anomaly for 5 year intervals from1880 to  2007

Global mean temperature time series from NASA

GCM structure and animation of GCM output

Summary of aquatic responses and climate envelope model studies

Ecological responses to climate change

Parmesan & Yohe 2003.  A globally coherent fingerprint of climate change impacts across natural systems.  Nature 421: 37-42.  (review of observed responses)

Examples of observed responses:

Fitter & Fitter 2002 - plant phenology (see fig 1 & table 1)
Diamond et al 2011 - butterfly phenology

1. Burkle et al. 2013.  Plant-pollinator interactions over 120 years: loss of species, co-occurrence, and function. Science 339: 1611-1615.

2. Edwards & Richardson 2004. Impact of climate change on marine pelagic phenology and trophic mismatch.  Nature 430: 881-884

Examples of
projections using the climate envelope approach:
3. Reusch et al.  2102. Projected Climate-Induced Habitat Loss for Salmonids in the John Day River Network, Oregon, U.S.A. Conservation Biology 26:873-882. (an excellent example of the climate envelope modellig approach
for three species)

Marine fish - interaction of climate effects on body size and extinction risk, accounting for changes in distribution

Thomas et al. 2004.  Extinction risk from climate change,  Nature 427: 145-148. (review of projections using climate envelope modelling and SA curves)


Study Guide. Broad topics are:
1. Fitting regression models appropriate to a data set, and interpreting results of that analysis.
2. Mechanisms of anthropogenic climate change
-properties of GH gasses
-disruption of carbon cycle
-effects on balance of incoming and outgoing EM radiation
3. Ecological responses to climate change:
-changes in community structure, trophic mismatch

The essay questions will be broad, show-what-you-know style questions.  The best answers will:
- be well organized and well written
- be clear and direct
- include supporting examples from class or the reading
- include verbal, graphical and algebraic explanations when possible.

5 Population Viability Analysis

A simple count based PVA assuming exponential growth,
using only the base functions in MS Excel.   Here is the same count based PVA in R, with some extensions.

Proof that geometric mean lambda and arithmetic mean r yield the same growth.

An illustration of the problems created by sampling error in estimates of N
-  false  density dependence
-  incorrect estimation of extinction risk

Lion example of limitations of direct estimation of lambda from count based approach.  Snare example 2.

Basic demography review and example with African wild dogs

Demographic PVA: Using Leslie matrix for age-structured population projection.
- creating the Leslie Matrix
- population projection with the Leslie Matrix

1. CWP CH. 5. 
2. CWP CH. 6.
3. CWP CH. 7.

Beissinger S & Westphal MI 1998.  On the use of demographic models of population viability in  endangered species management.  J. Wildl. Mgmt. 62:821-841 pdf  (BIOE 440 optional, BIOE 521 required)


USFWS information on Mountain Golden Heather

R Exercise Five: Estimating survival rates with Cormack-Jolly-Seber models

R Exercise Six
Stochastic Leslie matrix  projection v1:  .  The script 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).

HW 6

R Exercise Seven
 Stochastic Leslie matrix  projection v2:   Uses the popbio package to implement stochastic projection by treating each entry in the projection matrix as a distribution with a given mean and variance, and making a random draw from the distribution at each time step.

The take home exam will require you to begin with a demographic data set and modify one of the models of population dynamics to estimate extinction risk, using R.  T

Take Home Exam as Word file
Take Home Exam as pdf file.

6 Genetic Issues in Conservation

A. Speciation, classification and the ESA

 Linnaeus had no spam filter...
...more on Linnaeus's Kingdom Paradoxa

B. Hybridization (part 1), (part 2) including red wolf case study
C. Inbreeding  and F statistics, including cheetah case study
1. CWP CH. 3
2. Endangered Species Act (through page 14)

3. DPS policy from Federal Register
4. Allendorf et al. 2001.  The problems with hybrids: setting conservation guidelines.  Trends. Ecol. Evol. 16: 613-622.
5. Keller & Waller. 2002
Inbreeding effects in wild populations.  Trends Ecol Evol 17: 230-241.
Caro & Laurenson 1994.  Ecological and genetic factors in conservation: a cautionary tale.  Science 263:485-486.

HW 7: Inbreeding and F statistics

is 4:00 PM THURSDAY DEC 15th in 306 Lewis, mainly essay questions on new material, but will have  few short answer review questions on very major facts and concepts.

Final Exam study topics:

Genetic issues study guide

A few major facts to know:  How many people are in the world?  How many described species are there?  Very roughly, what fraction of all species are thought to be described now?  What is the atmospheric concentration of CO2?  What was it over the past 800,000 years prior to extensive use of fossil fuels?  How do current extinction rates compare to past rates?

With respect to conservation, are you a transcendentalist, a utilitarian, or a mixture of the two?  Why?