Conservation Biology, BIOE 440 and BIOE 521


Class Hours & Location: MWF 12:00- 12:50, Cheever Hall, Room 213

 

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

Software
:
Graduate students
:   We will use R to construct  simple mathematical models of population dynamics to estimate extinction risk.  I want to focus on the population biology (rather than the syntax) but it is also 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 and you can download it free 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. I strongly recommend Zuur, Ieno & Meester's "A beginner's guide to R".  "The R Book", by Crawley is a good comprehensive manual. I will provide example files that use R to model population dynamics in several different ways, and will have a few informal help sessions.


You can download a free copy of "A Beginner's Guide to R" using MSU's SpringerLink connection, as long as you are on an MSU-domain computer:
http://link.springer.com/book/10.1007/978-0-387-93837-0/page/1   (click the 'download book' link to get the entire thing as a pdf). 


The CRAN website has a link to many other open-access books on R:
http://cran.r-project.org/other-docs.html


Undergraduates:  We'll use MS Excel to  build simple mathematical models of population dynamics and estimate 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, making graphs, using formulas, copying and pasting in a way that maintains correct cell references (that is, understanding the use of "$" in cell references).  I will provide example spreadsheets  that use Excel to model population dynamics, which we will go over in class.


In Excel, press the F1 key to open the help system.  This will pop up a menu that is searchable, so for instance if you type "formula" into the search window, it will pop up a well-organized set of examples to explain the use of equations to calculate a value that is then inserted into a cell.


Grading:

BIOE 440: Two in class exams (15% each, one in finals week), a paper (15%), one take home test (15%), and 5-7 homework assignments (40%).  The take home test will be to construct a model to estimate a species' extinction risk from demographic data, using Excel.
BIOE 521:  Two in class exams (15% each, one in finals week), a paper (15%), one take home test (15%) 5-7 homework assignments (30%) and an in-class presentation (10%).  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), and you will present a 30 minute talk on a conservation issue of your choice (details below). 


Research Paper Instructions  Note that the assigment differs for BIOE 440 and 521.  You should look at the requirements, pick a topic and begin looking for articles with plenty of lead time.
The web page with instructions for the citation format has moved since I wrote the paper instructions.  The new address is: http://www.waikato.ac.nz/library/study/referencing/styles/animal-behaviour-style


In-class presentation (BIOE 521 only) evaluation form.  Broadly, your in-class presentation should be organized to accomplish the same goals laid out in points 3a-3d of the instructions for the research paper.  You will explain a general conservation issue/problem (to provide context for what follows), present the methods, results and inferences of a particular study (or perhaps a few studies), and then bring the talk full circle by succinctly explaining how that study(ies) advanced our understanding of the general issue. Broad - narrow - broad.  Bring the argument through a full circle.


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
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 Wildlife Populations, 2nd edition.  


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

1 Conservation Biology & Human population growth - a race between N & K. 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
3. (Optional for BIOE 440, required for BIOE 521) Balmford et al. 2002.  Economic reasons for conserving wild nature. Science 297: 950-953. pdf

HW1  (word docx file), PDF here


data set for HW1 from US Census of 2010.
2
Biodiversity: how many species, what patterns?  past and present extinction rates.

Just in time for the discussion of the number of species, a new carnivore species, the olinguito, has just been added! After we discussed this in class last year, 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

3
Designing and interpreting studies
1. CWP CH 2.
HW2

4

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


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

Global mean temperature time series from NASA






1. Pacala & Socolow 2004.  Stabilization wedges: solving the climate problem for the next 50 years with existing technologies.  Science 305: 968-972.

Ecological responses to climate change:

2. 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
3. Burkle et al. 2013.  Plant-pollinator interactions over 120 years: loss of species, co-occurrence, and function. Science 339: 1611-1615.

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

Examples of projections using the climate envelope approach:
5. 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 )
Wolverine climate envelope model
Marine fish - interaction of climate effects on body size and extinction risk, accounting for changes in distribution



EXAM
Friday 10/4 in class.  Study guide will be posted later today.


Study Guide.  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.

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

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

- BIOE 440: demographic PVA in Excel


BIOE 521: Stochastic Leslie matrix  projection v1:  (Code slightly updated 10/22/13 - to change some plotting commands that assumed you would not be using R studio).  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).

BIOE 521: Stochastic Leslie matrix  projection v2:  (Code slightly updated 10/22/13 to add a bit more annotation in comments explaining the loops.) 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.

1. CWP CH. 4
2. CWP CH. 5. 
BIOE 521 only : Read the beginning of CH 6 in A Beginner's Guide to R

for a description of 'for' loop structure (link to free pdf in the 'software' section above).
3. CWP CH. 6.
4. CWP CH. 7.

5.
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)














You must install the popbio package from a CRAN mirror site to run these R scripts.  In R Studio, click the 'packages' tab in the bottom right window, then click the 'install packages' menu option and type 'popbio' into the pop-up window that opens.

HW 3 due in class Wednesday 10/16












HW 4 due in class Friday 10/25







TAKE HOME TEST on PVA: passed out Wednesday 10/30 in class, due Friday 11/1 in class
BIOE 440 will use Excel, so familiarize yourself with the example Excel files for count based and demographic PVA to understand how they are implemented.

BIOE 521 will use R in the same manner.







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.
6.
Caro & Laurenson 1994.  Ecological and genetic factors in conservation: a cautionary tale.  Science 263:485-486.






HW 5: Inbreeding and F statistics, due in class FR 11/22

HW 5 KEY







Reminders:

Paper is due Wednesday 11/13 in clas

BIOE 521 presentations are in the week of 12/2/13:
I will have you sign up for time slots and give some more guidelines in class.

Final Exam is FR 12/13/13 at 8:00 am in regular room
Final is 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?

Briefly describe one of the graduate presentations, including the broad issue, the specific case, the primary methods, results and conclusions.