Conservation Biology, BIOE 440 and BIOE 521  
 

Class Hours & Location: MWF 12:00- 12:50, Monday and Friday: Lewis Hall Room 407.  Wednesday: 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 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). 


Software:
We will use the free software program to analyze data, and to construct  simple mathematical models of population dynamics to estimate extinction risk.  To conduct research in conservation biology and ecology these days it is essentially necessary to become familiar with R, because it is widely used for statistical analysis and mathematical modelling in ecology.  .  R is installed in the MSU student computer labs and you can download it free from the Comprehensive R Archive Network, CRAN.  We will be using 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: 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 also has links to other useful open-access books on R:
http://cran.r-project.org/other-docs.html


Grading:

BIOE 440: Three in-class exams (10% each, one in finals week), a paper (15%), one take home test (15%), and 7 homework assignments (40%). 


BIOE 521: Three in-class exams (10% each, one in finals week), a paper (15%), one take home test (15%), 7 homework assignments (30%) and an in-class presentation (10%).    The paper, the take-home exam (stochastic population modelling) and several of the homework assignments have extra requirements for graduate students (details below), and you will present a 30 minute talk on a conservation issue of your choice at the end of the semester (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 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. 
ABGR = Zuur, Ieno & Meesters, A Beginner's Guide to R.


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

ABGR CH 1
ABGR CH 2

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.

Look at R Exercise Two to do HW 1

HW1  (word docx file), PDF here
DUE Friday SEPT 5 in class





2
Biodiversity: how many species, what patterns?  past and present extinction rates.

Just in time for the discussion of the number of species in 2014: the bat out of hell (Murina beelzebub). In 2013, a new carnivore species, the olinguito, was 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

May 1988. How many species are there on earth? Science 241:1441-1449. (not assigned reading, just for background material in class).
Help Sessions will be Mon 3:00 in the Ecology Library (3rd floor Lewis Hall next to main office) and Wed 11:00 (307 Lewis).

Ryan Lamb's email is:
ryan.lamb2@gmail.com






EXAM 1: Monday SEPT 15 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.







3
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. 
BIOE521 - crowpies or your choice of anything else.


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.

ABGR CH 3
ABGR CH 4
ABGR CH 5

HW2A - OLS and GLM regression in R. Due Friday September 26th
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 Monday September 29th

HW3 - magpie data  Example data sheet.
Due Monday October 13th 
HW4 - magpie analysis  Due Wednesday Oct 22
BIOE 440 HW4 detailed description
BIOE 521 HW4 detailed description
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:
knp.allsp.oct2012.csv
knp_covs_oct2012.csv



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


NOAA - Atmospheric CO2 record

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

Global mean temperature time series from NASA


GCM structure examples one, two

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)









EXAM 2  Wednesday 10/15


Study Guide will be posted soon.  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:
-distribution
-abundance
-phenology
-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

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.

4.
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)


ABGR CH 6


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.







TAKE HOME TEST 
The take home exam will require you to begin with a demographic data set and modify the R models of population dynamics to estimate extinction risk.

Passed out 10/29, due 11/5.  Note different requirements for BIOE 440 and 521.







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 7: Inbreeding and F statistics

Key for HW 7







Reminders:

Paper is due Wednesday 11/12 in class

BIOE 521 presentations are in the final 4 sessions of class:
I will have you sign up for time slots and give some more guidelines in class.

Final Exam is MONDAY 12/8 at 4:00 in the 407 Lewis
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.