(GEO 4938/6938)
SYLLABUS 13 October 2009
Instructor: Michael W. Binford
Office Hours: Monday 4:00-5:00 PM, Thursday 2:00-3:00 PM; or By Appointment (e-mail me)
Office: 3139 Turlington Hall
Phone: 392-4652 ext 215 (although I do not use the telephone very much)
E-mail: mbinford@geog.ufl.edu
Required Textbook: Lomolino, M.V, B.R. Riddle, and J.H.
Brown. 2006. Biogeography. 3rd Ed. Sinauer
Recommmended Textbook:
Lomolino, M.V., D.F. Sax, J.H. Brown. 2004. Foundations of
Biogeography: Classic Papers with Commentaries. University of Chicago
Press. (also on reserve).
Class Meetings: Tuesday Periods 5-6 (11:45 - 1:40 P.M.), Thursday Period 6 (12:50 - 1:40 P.M.) in Turlington Hall, Rm. 3006.
Description: Biogeography is the science that describes and explains spatial patterns of biodiversity, and is core science in the understanding of human-environment interactions. Biogeographers study distributions of organisms, both past and present, and how related patterns of environmental variation influence the organisms. Recent new sciences of Landscape Ecology, Macroecology, and Global Ecology are extensions of or borrow significantly from Biogeography. Biogeography is also an applied science in that biogeography theory is useful for designing nature reserves, forecasting how climate change may affect organisms, and explaining human adaptations to environmental variability. This class will take a mostly ecological approach to understanding biogeography.
Prerequisites:
GEO 2200 Physical Geography or
Equivalent. Basic ecology and evolution would be useful but are not
required.
Course Objectives
- Undergraduate Section
1. Students learn the patterns and mechanisms of global to
local species distributions.
2. Students learn how to apply knowledge of biogeographic patterns and
mechanisms to solving important problems, e.g. biodiversity
conservation, forecasting responses of biota to environmental change at
scales from local to global.
3. Students generate an understanding of the hypothetico-deductive
scientific method: observations, theoretical explanation, testable
hypothesis generation, hypothesis testing, theory modification.
Educated skepticism will be enhanced.
4. Students learn the meaning of peer-reviewed, primary scientific
literature, and become familiar with reading and interpreting
scientific publications.
Basis of Grade -
Undergraduate Section:
1. Two equally weighted essay examinations (midterm and end of
semester), each worth 30% of the course grade.
2. One-paragraph summary of a peer-reviewed paper in
the current
scientific literature every other week weighted as one additional exam.
3. Class discussion participation weighted as 10% of the course grade.
Course Objectives
- Graduate Section
1. Students learn the patterns and mechanisms of global to
local species distributions.
2. Students learn how to apply knowledge of biogeographic patterns and
mechanisms to solving important problems, e.g. biodiversity
conservation, forecasting responses of biota to environmental change,
at scales from local to global.
3. Students conduct biogeographic literature research and analysis
necessary to develop excellent foundations for thesis and dissertation
research questions.
4. Students learn the classic literature in biogeography, and gain
experience leading discussions of this literature.
Basis of Grade -
Graduate Section:
1. Two equally weighted essay examinations
(midterm and end of
semester), each worth 25% of the course grade
2. Graduate students will collectively determine two "classic" papers
for each general topic, and each week one graduate student will lead
the class in a short discussion of the the "classic" papers of the
week, weighted as 25% of the course grade
3. Term paper (maximum
20 pages, 12-point font, double spaced, excluding figures,
tables, and references) on a biogeographic topic of the student's
choosing, weighted as 25% of the course grade.
Grades assigned as A = 90% and above, B+ = 88 - 89.9%, B = 80 - 87.9%, C+ = 78 - 79.9%, C = 70 - 77.9%, D+ = 68 - 69.9%, D = 60 - 67.9%, E = below 60%. No make-up exams will be given.
Please note that there are new policies for calculating grade point averages. See http://www.registrar.ufl.edu/catalog/policies/regulationgrades.html for details.
Schedule and Topics (Always
tentative except for dates of exams and assignments)
5 January Introduction, Course Logistics, Introduction to the Subject: The Science of Biogeography
7 January 1. History of Biogeography; Organization of Life and Codes of Zoological and Botanical Nomenclature 1. (ICZN website, IAPT - International Association for Plant Taxonomy web site)2. Organization of Life and Codes of Zoological and Botanical Nomenclature 2.
Lecture slides pdf file; Lecture slides 6/page pdf file
12 January Environmental Setting, The Geographic Template 1: Energy, Global Atmospheric and Oceanic Circulations, Global Distribution of Climates (Ch. 3)
Lecture slides pdf file; Lecture slides 4/page pdf file
14 January 1. Environmental Setting 3: The Geographic Template - A little more Climate; Soils (Ch. 3)
2. Environmental Setting 4: The Geographic Template - Aquatic Ecosystems (Ch. 3)
Lecture slides pdf file; Lecture slides 4/page pdf file
19January Distributions of Species: Ecological Foundations - Distribution Maps (Ch. 4)
Lecture slides pdf file; Lecture slides 4/page pdf file.
A GREAT source of range maps (as shapefiles) for animals and plants of the Western Hemisphere - this link is to bird families.
21 January 1. Map Representations - Projections/Coordinate Systems; Distributions of Species: Population Growth (Ch. 4)
Geographer's Craft web site for exploring various map projections.
2. Distributions of Species: Ecological Foundations - Competition, Predation, Mutualism, Parasitism, Pathogens (Ch. 4)
Lecture slides pdf file; Lecture slides 4/page pdf file.
Excellent web site for exploring various population models
Another good web site for exploring various population models
First literature summary due at 5:00 PM on 21 January. E-mail the pdf file of the paper and your summary to mbinford@geog.ufl.edu.
Literature Summaries
Student 1 Paper, Summary links
Student 2 Paper, Summary links
...
Student N Paper, Summary links
26 January Habitat Modeling, Predictive Vegetation Modeling pdf file; 4-slide/page pdf file.
Reading: 1. Review Franklin 1995 Predictive Vegetation Modeling. Prog. Phys. Geog.
2. Review Austin 2002 Spatial prediction of Species Distributions - ecological and statistical approaches. Ecol. Modeling
3. Example: Ohman and Gregory 2002. Modeling Forest Composition in Oregon. Can. J. For. Res.
4. Climate-change example Iverson and Prasad 1998 Predicting abundance of 80 tree species following climate change in E. U.S. Ecol. Monogr.
5. Review Miller, Franklin, and Aspinall 2007. Incorporating spatial dependence in predictive vegetation models. Ecol. Model.
6. USFWS Habitat Suitibility Index Model Newsom, J.D., T. Joanen, and R.J. Howard. 1987. Habitat suitability index models: American alligator. U.S. Fish Wildl. Serv. Biol. Rep. 8X10.136). 14 PP.
Web site for US Forest Service Climate Change Atlas: Predictive Vegetation Mapping, species by species
28 January 1 and 2. Habitat Modeling, Predictive Vegetation Modeling pdf file. 4-slide handout file
Reading - Classical Examples of Gradient Analysis - Whittaker and Niering 1975 Ecology
Reading - Complete GAP Analysis Handbook
2 February The Changing Earth 1 pdf file; 4-slide/page pdf file (Ch. 8)
4 February 1.The Changing Earth 2 (Ch. 8)
2. Glaciation and Biogeographic Dynamics of the Pleistocene (Ch. 9)
pdf file of slides for both lectures; pdf file of 4-slide/page handouts for both lectures
Second literature summary due at 5:00 PM on 4 February. E-mail the pdf file of the paper and your summary to mbinford@geog.ufl.edu.
Literature Summaries
Student 1 Paper, Summary links
Student 2 Paper, Summary links
...
Student N Paper, Summary links
9 February Glaciation and Biogeographic Dynamics of the Pleistocene pdf file; 4-slide/page pdf file (Ch. 9)
11 February 1 & 2. Glaciation and Biogeographic Dynamics of the Pleistocene pdf file; 4-slide/page pdf file (Ch. 9)
Interesting reading:
Davis, M.B. and R.G. Shaw. 2001. Range shifts and adaptive responses to Quaternary climate change. Science 292:673-679.
16 February 1. Glaciation and Biogeographic Dynamics of the Pleistocene: Two Important Issues - Tropical refugia in the Pleistocene and the Overkill Hypothesis. 4-slide/page handout pdf file. (Ch. 9 and readings).
Interesting readings:
2. Haffer, J. 1969. Speciation in Amazonian birds. Science 165:131-136
3. Knapp, S and J. Mallett. 2003. Refuting Refugia? Science (Perspectives): 300:71-72.
4. Martin, P.S. 1973. Discovery of America. Science 179:969-974.
5. Grayson, D. and D.J. Meltzer. 2003. A Requium for North American Overkill. Journal of Archaeological Science30:585-593.
6. Fiedel, S. and G. Haynes. 2004. A premature burial: comments on Grayson and Meltzer's "Requium for overkill" Journal of Archaeological Science 31:121-131.
18 February 1. Overkill Hypothesis (Ch. 9)
2. The Geography of Communities I ( Ch. 5)
Lecture slides pdf file; 4-slide/page lecture slide handouts pdf file.
Third literature summary due at 5:00 PM on 20 February. E-mail the pdf file of the paper and your summary to mbinford@geog.ufl.edu.
Literature Summaries
Student 1 Paper, Summary links
Student 2 Paper, Summary links
...
Student N Paper, Summary links
23 February The Geography of Communities II: PAR, Succession (composition, production), life forms, life zones pdf file, 4-slide/page pdf file. ( Ch. 5)
MID-TERM EXAM POSTED AFTER END OF LECTURE (Posted 5:29 PM), DUE 5:00 FRIDAY 26 FEBRUARY
Mid-term exam as .docx file; mid-term exam as .pdf file.
25 February 1. Climate Zones, Life Zones, Biomes pdf file; 4-slide/page handout pdf file
2 March Ecoregions, Other categorization of biotic spatial heterogeneity, Dispersal and Immigration pdf file; 4-slide/page handout pdf file (Ch. 6);
4 March 1. Dispersal and Immigration
2. Speciation and Extinction (Ch 7)
Lecture slides pdf file; 4-slide/page lecture slide handouts pdf file.
Fourth literature summary due at 5:00 PM on 4 March. E-mail the pdf file of the paper and your summary to mbinford@geog.ufl.edu.
Literature Summaries
Student 1 Paper, Summary links
Student 2 Paper, Summary links
...
Student N Paper, Summary links
6 March - 14 March SPRING BREAK
16 March Island Biogeography: Species Richness pdf file; 4-slide/page pdf file. (Ch. 13)
18 March Speciation (and Evolution) by Joe Townsend pdf file; 4-slide/page handouts pdf file
23 March Island Biogeography: Tests of Island Biogeography Theory and Lomolino's "New Paradigm" pdf file; 4-slide/page handout pdf file
1. Simberloff and Wilson. 1969. Experimental Zoogeography of Islands: The Colonization of Empty Islands. Ecology 50:278-296.
2. Wilson, E.O. and D.S. Simberloff. 1969. Experimental Zoogeography of Islands: Defaunation and Monitoring Techniques. Ecology, Vol. 50:267-278
3. Simberloff, D. 1976. Species Turnover and Equilibrium Island Biogeography. Science 194:572-578
4. Simberloff, D. 1974. Equilibrium theory of Island Biogeography. Annual Review of Ecology and Systematics. V. 5:161-182.
5. Simberloff, D. and L. Abele. 1976. Island biogeography theory and conservation practice. Science 191:285-286.
6. Walter, H. 2004. Mismeasure of Islands: implications for biogeographical theory and the conservation of nature. J. Biogeography 31:177-197.
6. Gilbert, F.S. (1980) The equilibrium theory of island biogeography: fact or fiction? J. of Biogeography, 7, 209–235.
25 March Island Biogeography: Assembly of Island Communities pdf file; 4-slide/page handout pdf file (Ch. 14)
Fifth literature summary due at 5:00 PM on 25 March. E-mail the pdf file of the paper and your summary to mbinford@geog.ufl.edu.
Literature Summaries
Student 1 Paper, Summary links
Student 2 Paper, Summary links
...
Student N Paper, Summary links
30 March Assembly of Island Communities amd Evolution of Island Communities pdf file; 4-slide/page handouts pdf file (Ch. 14)
1 April Areogeography, ecogeographic rules 4-slide/page pdf file.
6 April Diversity Gradients (Ch 15) pdf file; 4-slide/page handout.
8 April Biodiversity and Geography of Extinctions (Ch. 16) pdf file; 4-slide/page handout.
Sixth literature summary due at 5:00 PM on 9 April. E-mail the pdf file of the paper and your summary to mbinford@geog.ufl.edu.
Literature Summaries
Student 1 Paper, Summary links
Student 2 Paper, Summary links
...
Student N Paper, Summary links
13 April Conservation Biogeography I (Ch. 17)
15 April Course Evaluation
Conservation Biogeography II: Return to Predictive Vegetation Mapping as a Conservation Tool (Ch. 17)
20 April Human Biogeography; Wrap-up pdf file. 4-slide/page handout pdf file.
Second Exam: XX April XX:00-XX:00
EXAMS
Mid-term and end-of-semester essay exams will
evaluate the ability of the student to understand and synthesize the
material presented in class and in the reading. Students are
responsible for all material in lectures and readings.
BI-WEEKLY SUMMARIES OF PEER-REVIEWED PAPERS IN THE CURRENT
SCIENTIFIC LITERATURE
Every other week undergraduate students will read a
peer-reviewed paper in the current scientific literature and hand in a
summary of the paper and a pdf file of the paper. "Current" means
published in the past 4 years
(2005-2009 or 2010 for Spring 2010). The summary will state 1) The full
citation reference for the study, 2) the research problem
or question (1 or 2 sentences), 3) the general background knowledge
leading up to this study (2 sentences), 4) the methods used by the
investigators (1 or 2 sentences), 5) the results of the study (2
sentences and one figure or table), 6) what are the weaknesses of the
study, and 7) what we learned new from the
study (2 sentences). This is a total of 12 sentences at most and one
illustration of the evidence and is not
a copy of the abstract
of the paper. Here
is an example of a paper that would be
appropriate, and here is an
example of the summary of the paper (NOTE: I ADDED A SHORT SECTION
AT THE END "MWB Comments" THAT DESCRIBE SOME OF MY THINKING THAT WAS
NOT ADDRESSED IN THE PAPER ITSELF. YOU DON'T HAVE TO WRITE THIS UNLESS
YOU WANT TO.). Each summary will be evaluated
on the basis of how well it describes the paper. The
overall grade on the summaries will be equivalent to one exam.
CLASSIC WORKS IN BIOGEOGRAPHY
Every topic in any discipline has seminal
papers or books that started research programs or changed the way that
scientists, and ultimately the public, understand their subject. These
publications are often called "classic" works. Examples in Biogeography
include Darwin's "On the Origin of Species," Wallace's "The
Geographical Distribution of Animals," Dov Por's "One Hundred Years of
Suez Canal -- A Century of Lessepsian Migration: Retrospect and
Viewpoints," Elton's "Ecology of Invasions by Animals and
Plants," Haffer's "Speciation in Amazon Forest Birds," MacArthur
and Wilson's "Island Biogeography," and many others. Lomolino et al.
(2004) "Foundations of Biogeography: Classic Papers with Commentaries"
(on reserve in the Marston Science Library for the semester) is a great
source of these papers, and although it is very long it does not have
all of the papers that you might consider "classic."
Lomolino et al. (2004) recognize eight
general topics within which classic papers are identified: 1. Early
Classics; II. Geological history and the distribuion of species; III.
Biological and environmental factors affecting species' ranges, issues
of scale, human influences; IV. Revolutions in Historical Biogeography,
geography of dispersal, phylogenetic systematics, V. Geography and
diversification, VI. Island biogeography, human effects on extinctions;
VII. Community assembly rules; VIII. Environmental gradients and
species diversity. To this I would add IX. Conservation biogeography.
Each graduate student will select one of
the topics, and 2-3 papers within the topic, to summarize for the rest
of the class in a short written paper that the class will read and a
short in-class presentation and discussion. The summary, presentation,
and discussion will account for 25% of the graduate student's grade for
the course.
TERM PAPER
EXTRA CREDIT
Many students, both graduate and undergraduate, are involved with independent study projects, thesis or dissertation research, or have other experiences with biogeographic research. Short (10-minute) presentations to the class that describe these projects or experiences will be welcome, and will earn extra credit. Past presentations have included a description of a colonization study of small aquatic ecosystems and the Ordway-Swisher Biological Station and a description of a study of the genomes of all terrestrial and marine species that live within 1 km of the land-water interface in Moorea.
LINKS TO VARIOUS JOURNALS WITH BIOGEOGRAPHIC CONTENTS
General Biogeography
Academic
Honesty,
Student Responsibilities, Student Conduct Code, etc.
Students are required to do their own work
on the exams,
for term papers, and for the literature summaries. It is fine to
consult with each other on how to
make
measurements, where to find interesting literature, etc., but each of
you must submit your own work
separately. The penalty for
cheating
is to receive zero points for that exam or paper, and the incident will
be reported to the Student Honor Court. You are required to review the
UF Student Responsibilities Guidelines (links below).
- Academic Honesty
- Student Conduct Code
- Alcohol and Drugs
- Relations Between People and Groups
- Service to Others
- Standard of Ethical Conduct
Students requesting classroom accommodation must first register with the Dean of Students Office. The Dean of Students Office will provide documentation to the student who must then provide this documentation to the Instructor when requesting accommodation.