Conservation Biology, BIOE 440 and BIOE 521

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.

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

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.

**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

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.

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.

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 4 due in class Friday 10/25

BIOE 521 will use R in the same manner.

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

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

Paper is due Wednesday 11/13 in clas

BIOE 521 presentations are in the week of 12/2/13:

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

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.