Robert P. Anderson, Ph.D.
Graduate Zoogeography
seminar
Spring 2008
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- Biology V9012/79012,
Seminar in Zoogeography, 3 credits (Graduate course)
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- Time: Monday, 2:00–5:00 p.m.
- Location: CUNY
Graduate Center, Room C415B (365 Fifth Avenue, at 34th Street)
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- Instructor: Dr. Robert P. Anderson, Assistant Professor,
City College of CUNY
- Office: J-817 Marshak Science Building, CCNY; Telephone:
212-650-8504
- Office hours: Wednesday, 10:00 a.m.-1:00 p.m. or by
appointment
- E-mail: anderson@sci.ccny.cuny.edu
(for scheduling issues)
- Webpage: http://web.sci.ccny.cuny.edu/~anderson/
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Download
syllabus
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Course
philosophy:
This graduate seminar will cover the
conceptual basis and practical application of GIS-based techniques for
modeling species distributions based on occurrence records and digital
environmental data. Specifically,
we will focus on the problem of modeling species geographic distributions
using presence-only data (where occurrence records are available, but no
data exist regarding absences). Despite
the title of the course, these techniques are general with regard to taxon
(i.e., applicable both plants and animals).
Furthermore, they can be applied at any spatial scale, using a grain
and extent relevant to the problem at hand.
The course is designed for students with a specific research interest
in using presence-only distributional modeling.
The
format will include both lecture/discussion and exercises on individual
computers. We will read
selections from the primary literature, and students will conduct a research
project using their own data. During
the semester, students will give regular updates on the progress of their
project. A few leaders in the
field who work in the New York metropolitan region may give guest
presentations.
Grading:
Students will be evaluated based on class participation (including
short presentations) and the research project.
Plagiarism will be dealt with subject to CCNY/CUNY policies.
Absences:
Attendance
is required. Excused absences
must be documented (e.g., death in the family, extreme sickness, etc.).
Absence from more than 2 class periods can result in your being
dropped from the course for excessive absences (WU).
Tentative
schedule (may be modified if necessary):
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Date
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Topic
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Exercises
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Project presentation
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Mon.
28 Jan.
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Introduction to
modeling species distributions
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Introduction to DIVA
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Share research interest
in distributional modeling
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Mon.
4 Feb.
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Presence-only
occurrence data
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DIVA tutorial
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Present background to
research project
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Mon.
11 Feb.
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Environmental data for
distributional modeling
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DIVA tutorial
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Show occurrence data
for project
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Mon.
25 Feb.
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Introduction to
presence-only modeling techniques
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BIOCLIM modeling in
DIVA
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Show environmental data
for project
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Mon.
3 Mar.
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Introduction to Maxent
modeling
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Maxent tutorial
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Show BIOCLIM models
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Mon.
10 Mar.
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Model evaluation 1:
threshold-dependent evaluations (e.g., binomial)
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DIVA tutorial and
Maxent tutorial
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Show Maxent models
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Model evaluation 2:
threshold-independent evaluations (e.g., AUC/ROC)
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DIVA tutorial and
Maxent tutorial
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Show
threshold-dependent evaluation statistics for models
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Wed.
26 Mar.
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Advanced Maxent
modeling (e.g., selecting study region, selecting feature classes, and
tuning regularization)
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Maxent tutorial
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Show
threshold-independent evaluation statistics for models
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Postprocessing:
considering sampling adequacy and biotic and historical restrictions
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Show experiments
varying advanced aspects of Maxent modeling
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Mon.
7 Apr.
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Applications 1 (e.g.,
climate change, conservation/reserve design, invasive species, niche
evolution)
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Show final data and
plan for research project
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Mon.
14 Apr.
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Applications 2
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Share
problems/challenges encountered
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Mon.
28 Apr.
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Applications 3
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Share
problems/challenges encountered
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Mon.
5 May
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Presentations 1
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Present final project
results (some students)
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Mon.
12 May
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Presentations 2
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Present final project
results (remaining students)
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Tentative
schedule of readings (may be modified if necessary):
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Date
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Topic (abbreviated)
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Primary readings (read before)
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Other readings (read after for
student-led discussion the following week)
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Mon.
28 Jan.
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Introduction
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Graham et al. 2004 (TREE);
Wiens and Graham, 2005
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Mon.
4 Feb.
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Occurrence data
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Soberón and Peterson,
2004
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Graves 2000; Guralnick
et al., 2006; Stein and Wieczorek, 2004
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Mon.
11 Feb.
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Environmental data
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Hijmans et al., 2005
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Mon.
25 Feb.
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Modeling techniques
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Busby, 1986; Elith et
al., 2006
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Araújo and Rahbek,
2006; Hernandez et al., 2006; Pulliam, 2000
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Mon.
3 Mar.
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Maxent modeling
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Phillips et al., 2006
(part)
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Mon.
10 Mar.
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Evaluation 1
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Fielding and Bell,
1997; Liu et al., 2005
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Anderson et al., 2003;
Pearson et al., 2007
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Evaluation 2
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Hanley and McNeil,
1982; Zweig and Campbell, 1993
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Boyce et al., 2002
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Wed. 26
Mar.
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Advanced Maxent
modeling
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Phillips et al., 2006
(part); Zaniewski et al., 2002
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Postprocessing
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Mackey and Lindenmayer,
2001
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Anderson, 2003;
Anderson et al., 2002; Peterson et al., 1999
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Mon.
7 Apr.
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Applications 1
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TBA (student-selected)
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Mon.
14 Apr.
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Applications 2
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TBA (student-selected)
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Mon.
28 Apr.
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Applications 3
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TBA (student-selected)
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Mon.
5 May
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Presentations 1
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None.
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Mon.
12 May
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Presentations 2
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None.
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Examples
of applications readings (to be selected by students): Graham
et al., 2004 (Evolution); Pearson and Dawson, 2003; Peterson, 2003;
Peterson and Holt, 2003; Sánchez-Cordero
et al., 2005
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R. P. Anderson
Copyright © 2008.
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All photographs by RPA
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Last modified: 26 January 2008 (RPA)
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