VERTEBRATE POPULATION DYNAMICS

FNR 547

COURSE DESCRIPTION: Introduction to mathematical models of population processes; analysis and estimation of spatial and temporal variation in population-level parameters of vertebrates; computer modeling of populations; quantitative basis for conservation and management of populations.

INSTRUCTOR: Dr. Patrick Zollner TEACHING ASSISTANT: Joe Duchamp

Office: Forestry Building, Room 102A Office: Forestry Building, Room 204

Phone: 49-43590 Phone: 49-61216

Email: pzollner@purdue.edn Email: jed@fnr.purdue.edu

Hours: MWF 3:30-4:20, or by appointment Hours: M 12:40-1:30 F 3:30-4:20 or appt.

TEXT: Finally a book has been written for the material covered in this course. “Analysis and management of animal populations” by Williams, Nichols, and Conroy provides a detailed treatment of vertebrate population dynamics. It is destined to become a valuable resource that should be on the shelf of every wildlife biologist. Don’t sell it back if you intend to stay in the wildlife profession. As a supplement, I have provided a list of books that you may find useful as reference materials; most of them can be found in the Life Science library in Lilly Hall. I also have provided citations from the primary literature pertaining to topics that we examine. I encourage you to explore these references in more detail than we can cover in class. Students are expected to come to class prepared; in other words, read the required material before the lecture, and be prepared to ask (and answer) questions about it.

ATTENDANCE: I do not regularly record attendance, but attendance and final course grades are significantly correlated.

HOMEWORK: Problem sets and assignments for computer modeling will be made regularly throughout the semester. Answers to problems should be neatly written, with sufficient text to enable me to follow easily the line of reasoning used to solve a problem. All work which is germane to a solution should be shown; i.e., provide intermediate steps in simplifying a complex algebraic expression, but don't clutter the page by including "dead end" calculations. And organize your answers; if you hand in a messy, jumbled draft that skips from one part of a page to another, you will lose points. Partial credit will be given only sparingly if at all, so check your work and avoid silly mistakes. A penalty of 10% per class day is assessed to any late assignment.

POLICY ON CHEATING: Each student is expected to do his/her homework independently, except as outlined below. I encourage discussion of approaches or difficulties encountered when solving homework problems. However, each student is responsible for deciding upon an approach and for completing the necessary calculations. In other words, any form of copying or group problem-solving constitutes cheating. Periodic visits will be made to the student commons and the computer lab to monitor compliance. Cheating will result in a zero for the assignment in question. A second offense will result in a zero for the course. Do your own work; you'll learn more and be prouder of your accomplishments!

FNR 547 SYLLABUS

DAY	DATE	READINGS/ DEADLINES	TENTATIVE TOPIC
M	25 Aug	Chap 1	Introduction and course overview
W	27 Aug	Self-assessments Chaps 2, 3	Scientific method and the role of models
F	29 Aug	Chap 4	Statistics and parameter estimation
M	1 Sep		Labor Day – no class
W	3 Sep	Chap 4	Parameter estimation and hypothesis testing
F	5 Sep	Chap 5	Sampling designs for population studies
M	8 Sep	Chap 5	Sampling designs for population studies
W	10 Sep	Chap 12	Canonical estimator for abundance from counts; Population indices
F	12 Sep	Problem ID Chap 13	Estimating abundance: distance-based methods
M	15 Sep	Chap 13	Estimating abundance: distance-based methods
W	17 Sep	Chap 14.4-14.5	Estimating abundance of closed populations subject to exploitation
F	19 Sep	AGAD 021	Tutorial: SPSS and DISTANCE
M	22 Sep	AGAD 021	Tutorial: MARK (Huggins design)
W	24 Sep	Chap 14.1-14.3	Estimating abundance of closed populations with mark-release-recapture
F	26 Sep	Chap 14.1-14.3 Team Charter Due	Estimating abundance of closed populations with mark-release-recapture
M	29 Sep		Estimating abundance with telemetry and resighting data
W	1 Oct	Chap 15	Estimation of survival using telemetry or nest searches
F	3 Oct	AGAD 021	Tutorial: MARK (CAPTURE) Tutorial: NOREMARK
M	6 Oct	Chap 15	Estimating survival using telemetry or nest searches
W	8 Oct	Chap 17	Estimating survival from mark-release recapture studies
F	10 Oct	Study Design Chap 17	Estimating survival from mark-release recapture studies
M	13 Oct		October Break – no class
W	15 Oct	Chap 16	Estimating survival from band-return data
DAY	DATE	READINGS/ DEADLINES	TENTATIVE TOPIC
F	17 Oct	AGAD 021	Tutorials for survival: MARK (Mayfield, Known Fates design), MICROMORT, SPSS
M	20 Oct	AGAD 021 Study Design Peer Evaluation	Tutorials for survival: MARK (Cormack-Jolly-Seber, band-recovery designs)
W	22 Oct	Chap 18	Estimating abundance and recruitment from MRR studies
F	24 Oct	Chap 19	Combining open and closed MRR models: the Robust Design
M	27 Oct	AGAD 021	Tutorials for survival: MARK (Jolly-Seber, Pollock’s robust design)
W	29 Oct	Chap 20	Estimating community parameters from MRR studies
F	31 Oct	AGAD 021	Tutorial for community parameters: MARK and COMDYN
M	3 Nov		Quantifying habitat selection
W	5 Nov		Estimating home-range size
F	7 Nov	Chap 8.1	Density-independent population models
M	10 Nov	Chap 8.2	Density-dependent population models
W	12 Nov	Chap 8.4	Age-structured population models
F	14 Nov	AGAD 021	Tutorial: POPULUS
M	17 Nov	Original MS Chap 8.4	Age-structured population models and Lotka’s equation
W	19 Nov	Chap 8.5	Size-structured population models
F	21 Nov	AGAD 021	Tutorial: MATLAB
M	24 Nov	Peer Reviews Chap 8.4-8.5	Parameterizing Leslie and Lefkovitch matrices
W	26 Nov		Thanksgiving Break – no class
F	28 Nov		Thanksgiving Break – no class
M	1 Dec	Chap 11.1	Dynamics of harvested populations
W	3 Dec	Chap 11.2	Spatially structured models and conservation
F	5 Dec	Revised MS	Human population growth and a responsibility philosophy
	TBA	Final Exam

SEMESTER PROJECT:

The semester project is actually broken into two parts. The first part requires you to work individually to identify important research problems related to the management and understanding of vertebrate populations and to design a study to address a particular problem that is assigned to you. You also will critique (anonymously) one of your peer’s study designs. In the second part of the project you will work as a member of a team to which you are assigned. Your task will be to test particular hypotheses using real data and appropriate quantitative methods from those covered in class. Your team will be responsible for handing in a scientific manuscript detailing your work, evaluating manuscripts written by other teams, and presenting an oral report summarizing your findings.

Individual Portion

• Skills Assessment – Fill out the form on WebCT and return it on the second day of class.
• Problem Identification – You are required to identify two (2) "real-world" questions or problems related to vertebrate population dynamics. How should you come up with a question or problem related to population dynamics? First, look at the syllabus and listen to the description of topics covered in the course. Although the course is by no means an exhaustive treatment of topics in population dynamics, it's a good start. Next, look at the table of contents of your textbook and consult one or more of the supplemental texts and suggested references from the primary literature. Third, browse through recent issues of technical journals (e.g., Conservation Biology, Journal of Wildlife Management, Ecology, Ecological Applications, Journal of Animal Ecology, etc.) as well as the journals related to a specific vertebrate taxon (e.g., Journal of Mammalogy, Auk, Condor, Copeia, Journal of Herpetology, Transactions of the American Fisheries Society) to get ideas. Remember that you're dealing at this stage with concepts and ideas, so don't limit yourself taxonomically (if you find an interesting idea in a bird journal, it may well apply to fish, mammals, or herps). Fourth, conduct key word searches in electronic bibliographic data bases.

Important: choose a problem or question that is of importance to vertebrate ecologists and managers. The problem ultimately should be explained and then summarized with objectives or hypotheses to test.

• Study Design – After important problems have been identified, a subset of those will be selected (by me). Each student will be randomly assigned a problem for which he/she will be responsible for designing a study that addresses the objectives/hypotheses related to the problem. The design should be detailed and specific. It should include biological and budgetary considerations.
• Evaluation of Peer Design – You will be responsible for critiquing a study designed by one of your classmates. Anonymity will be preserved by assigning student designs a random number known only to me and the teaching assistant. You will be graded on your critique, so take it seriously.

Team Portion

• Original Manuscript – You will be assigned to a team based on analysis of the skills assessment. Each team will receive a real data set and a list of questions or hypotheses pertaining to the data. An explanation of the data, including the manner in which they were collected, will be provided. Every effort will be made to ensure that all data sets used are comparable in terms of their complexity. Data sets will be allocated to teams randomly. Although our goal is to assign each team a different data set, duplicate sets may be used occasionally. The task of each team is to analyze the data set using appropriate methods so that the questions/hypotheses are addressed. Results of your efforts will be a scientific manuscript that reports your findings and discusses its implications. The manuscript should be presented in the format of The Journal of Vertebrate Population Dynamics. The structure of the paper typically will be: Abstract, Introduction, Methods, Results, Discussion, and Literature Cited. Tables and figures are permissible (and probably necessary). Detailed instructions for preparation of your report have been provided on the course website.
• Written Reviews of Other Manuscripts – One copy of the original manuscript (with your name on it) will be graded by me. The other two copies (without your name) will be distributed to two other teams who will serve as reviewers. Thus, each team will serve as a reviewer of two manuscripts. Reviewers should treat the manuscripts as confidential, and read them as though they have been submitted for publication to a scientific journal. Rating forms and comment sheets for reviewers, modeled after those used in professional ecological and management journals, will be available on the course web site. Briefly, reviewers should remain anonymous and objective, providing constructive criticism (and praise) as warranted. Each team will be graded on the quality of their reviews.
• Final Revised Version of Manuscript – After receiving the reviewer comments, your team will prepare a final version of your report to hand in [one paper copy and one disk copy (floppy, zip or CD)]. Disk copies of tables and figures also should be submitted at this time.
• Oral Presentation – Your final version will serve as the basis for an oral presentation, to be presented as part of a public symposium held in the evening during the last week of the semester.

% OF PROJECT

PROJECT GRADE BREAKDOWN GRADE

Questionnaire for team skills assessment .................................................................... 1

Problem ID ................................................................................................................ 4

Study Design …….................................................................................................. 20

Evaluation of peer design............................................................................................ 10

Original version of manuscript: 3 copies of manuscript (1 with name on it) ............... 30

Written reviews of other team reports ........................................................................... 10

Final (revised) version of manuscript: 1 paper copy and 1 disk copy .......................... 15

Oral report .................................................................................................................... 10

COURSE GRADE: A final course grade will be calculated from homework assignments and the semester report according to the following formula:

HOMEWORK = 55%

SEMESTER PROJECT = 35%

FINAL EXAM = 10%

Each homework assignment will be weighted equally. A final grade of 90-100% will earn an A, 80-89.9% no lower than a B, 70-79.9% at least a C, and 60-69.9% at least a D. I rarely curve.