Geography 323: Biogeography

Fall 2024

Lecture: Tuesday & Thursday 2:00-3:20 in 101 Knight Library

Weekly lab sections, one hour: ---- in 206 Condon.  Some will be held outdoors on campus.

Instructor: Dan Gavin (dgavin@uoregon.edu)
Phone: 541-346-5787 (messages will be forwarded to me)

Office Hours: Mondays 2:00-3:00 in Pacific 217A. Or by appointment. There will be a Zoom option for joining office hours each week (see Canvas announcements).

Graduate teaching assistant: Geoffrey Johnson
Office hours Tuesdays 3:30-4:30 in Pacific 217

Course Overview:  The spatial patterns of species distributions are widely recognized, but few appreciate the complex causes of these patterns.  Biogeography is the study of the spatial patterns of biological diversity, and its causes, both in the present and in the past. Biogeographers synthesize information from a very broad range of fields, including ecology, evolution, paleontology, and climatology. This course will provide the ecological and historical foundations for understanding the distribution and abundance of species, and the changes in distribution and abundance over time.  We will also explore the relevance of biogeography during a time of increasing human impact and climate change.

Prerequisite: GEOG 141 or ERTH 103 or ERTH 203 or BI 370.

The course begins with an overview of important concepts, including evolutionary mechanisms, earth history, and plate tectonics, as well as concepts of the ecological niche and patterns of distribution at various taxonomic levels.  We also study basic ecological concepts, how species are patterned and disperse on the landscape, and how these patterns have changed over the relatively recent ice ages.  In the second part of the course, we delve into historical biogeography and study why continents and islands have unique assemblages of species, and the effects of mega-extinctions and biotic interchanges between continents. We also return to ecological concepts in a detailed examination of the equilibrium theory of island biogeography.  The following diagram illustrates the organization of topics to be covered, with the emphasis on how this information is used to understand current biodiversity and what threatens it.

Goals of the course

• To develop an appreciation for the historical and ecological factors that influence the pattern of life on earth.
• To survey the scientific revolutions of evolution, plate tectonics, and molecular ecology that shaped the path to modern biogeography.
• Using the lab assignments, to understand the scientific method and how to test hypotheses using inferential statistics.
• To understand the processes that affect how biotas respond to a changing climate, and the challenges we face today and in years to come.

Core Education fulfillment

This course is designated as a Natural Science Core Education course. At UO, core education is designed to provide a broad, interdisciplinary education that helps students, think critically and creatively, communicate clearly, and reflect ethically. Specifically, in this class, you will learn and practice critical thinking through a lecture content emphasizing how different disciplines converge in the topic of biogeography, and in the data and observations you make in your lab assignments, and creative thinking through several opportunities to generate hypotheses around observations in your five lab assignments.

Course modality

This is an in-person course: that means that, unlike asynchronous online/ASYNC WEB courses, we will meet during scheduled class meeting times in (class location). I will accommodate absences as described in the Absences policy below. If you need additional flexibility, UO encourages you to consider ASYNC WEB courses. If you need accommodation related to a medical or other disability, you can request those by working with the Accessible Education Center.

Technical Requirements

• Canvas is the place to go for course information and engagement outside of class time. To access our course Canvas site, log into canvas.uoregon.edu using your DuckID. If you have questions about using Canvas, visit the Canvas support page. Canvas and Technology Support also is available by phone (541-346-4357) or by live chat on the Live Help webpage.
  
• Laboratory assignments require a web browser and Google Earth desktop software. Google Earth is not available on Chromebooks. It is available on computers in the Knight Library and elsewhere on campus.

How will I communicate with you?

• Our class will communicate through our Canvas site. Announcements and emails are archived there, automatically forwarded to your UO email, and can even reach you by text. Check and adjust your settings under Account > Notifications.
• Every Monday I will post an Announcement that previews critical concepts we'll work on that week and a checklist of the week's due dates. You can also find this information in the overview page in each Canvas module.
• When I need to get in touch with individual students, I do so through email.
• The GE will be using the same Canvas site used for the entire course.
• How can you communicate with me? If your question (or comment) is
  • a practical, yes/no one about an assignment, reading, or other component of our class, please post your question on the Discussion thread titled "Class Questions and Answers," which I respond to daily, and where your peers can also pose questions and share answers.
  • about a technical challenge with Canvas or another technology, please contact the UO Service Portal.
  • about course content or activities, about something personal, time sensitive, or something else that doesn't feel like it fits above, please reach out to me by email or by attending office hours!
• I try to respond to questions within one business day.
• Why should you communicate with me? I enjoy talking with students about our course material! Are you confused or excited about something? Wondering how what we're learning relates to current events, career choices, or other classes you can take UO? Please be in touch! Please also be in touch to tell me how you are doing in the course. If you are having trouble with some aspect of it, I would like to strategize with you. I believe every student can succeed in this course, and I care about your success.
• Office hour details: Please see the top of the syllabus. I welcome meetings outside my regular office hours as well. Just email me to set a time.
• What: During office hours, students bring in a wide range of concerns, questions, and successes. We might talk through a specific concept or problem to clarify it, might think together about an issue a student is curious about that relates to the class, might discuss a student's post-graduation goals, might identify more supportive methods to study for a future exam or to begin a project, or any number of other topics. Some students have never been to an instructor's office hours. If that is you, please change that this term by attending! Feel free to come with a peer if that is useful for you.

Classroom community expectations

• All members of the class (both students and instructor) can expect to:
  • Participate and Contribute: All students are expected to participate by sharing ideas and contributing to the learning environment. This entails preparing, following instructions, and engaging respectfully and thoughtfully with others.
  • While all students should participate, participation is not just talking, and a range of participation activities support learning. Participation might look like speaking aloud in the full class and in small groups as well as submitting questions prior to class or engaging with Discussion posts.
  • Expect and Respect Diversity: All classes at the University of Oregon welcome and respect diverse experiences, perspectives, and approaches. What is not welcome are behaviors or contributions that undermine, demean, or marginalize others based on race, ethnicity, gender, sex, age, sexual orientation, religion, ability, or socioeconomic status. We will value differences and communicate disagreements with respect. We may establish more specific guidelines and protocols to ensure inclusion and equity for all members of our learning community.
  • Help Everyone Learn: Part of how we learn together is by learning from one another. To do this effectively, we need to be patient with each other, identify ways we can assist others, and be open-minded to receiving help and feedback from others. Don't hesitate to contact me to ask for assistance or offer suggestions that might help us learn better.
  • Guidelines for using Canvas Discussion:
    • Use subject lines that clearly communicate the content of your post
    • Write concisely, and be aware that humor or sarcasm doesn't always translate in writing.
    • Be supportive and considerate when replying to others' posts. This means avoiding use of jargon or inappropriate language, and it means disagreeing with respect and providing clear rationale or evidence to support your different view.
    • Keep focused on the topic and reference readings and other class materials to support your points (as applicable).
    • Try to use correct spelling and grammar and proofread your submissions. After submitting, use the edit feature to make corrections and resubmit (don't create a new or duplicate post that corrects your error).

Academic integrity

The University Student Conduct Code defines academic misconduct, which includes using unauthorized help on assignments and examinations, the use of sources without acknowledgment, and recording class without the express written permission of the instructor(s). Academic misconduct is prohibited at UO. I will report all suspected misconduct to the Office of Student Conduct and Community Standards. If the Office finds a student has committed misconduct, consequences can include of the relevant assignment or exam, or of the course.

While unauthorized help and use of sources without citation is prohibited, learning together and citing sources is crucial! For each assignment, you may help each other by discussing the graphs and plots of data, but assignements should be written entirely on your own. Citation methods are provided in the writing guide for the lab assignments.

If at any point in the term you are unsure about whether a behavior aligns with academic integrity in our course, please contact me. I view student questions about academic integrity as a desire to act with integrity, so I welcome your questions.

Student experience surveys

The midway and end-of-term Student Experience Surveys occur on week 4 and week 10. I do not devote class time to these activities but I still highly value your input. These are important opportunities to provide feedback about your learning experiences. I value this feedback and am continually improving the course with students' responses in mind. The key parts of the survey are the open-ended questions where you share concrete, actionable feedback and about the teaching practices that stand out to you. Thank you for your thoughtful reflections!

Absences

• Lectures
  • Attendance will not be taken during lecture and you do not need to notify me if you will be missing lecture.
  • Lecture notes are posted on Canvas for some of the topics presented in class. However, the notes are not comprehensive. The note should help you understand which parts of the readings were emphasized in the class that you missed.
  • In cases of extensive absences, I do not reach out to you to remind you of due dates or implications for your grade. You are responsible to understand the deadlines for withdrawal and grade change (to P/NP, for instance), or how to petition for changes.
  • It is generally expected that class will meet unless the University is officially closed for inclement weather. If it becomes necessary to cancel class while the University remains open, this will be announced on Canvas and by email. Updates on inclement weather and closure are also communicated as described on the Inclement Weather webpage.
• Labs/discussion sections
  • If you cannot make it to your lab meeting for whatever reason the first option is to ask the teaching assistant if you can switch to a different one-hour section that fits with your schedule.
  • If you must skip the lab meeting (for example, illness), you will miss important information and data-gathering to complete the assignment. You will need to get this information from other students in the class or from the GE/teaching assistant during their office hours. Please make every effort to attend these sessions as the assignments have multiple steps and understanding the expectations and how to complete the assignment will be more clearer!

Artificial intelligence use

Use of artificial intelligence systems (e.g., ChatGPT, iA Writer, etc.) is allowed provided you note explicitly where in your work process you used AI (e.g. generating an outline or first draft) and which platform(s) you used. If you use text generated by an artificial intelligence system as part of an assignment submission, such as a paper, you must attribute the text to the AI-based system that is its source. For example, if you include text generated by ChatGTP, you must cite the source as follows:

ChatGPT. (Year, Month, Day of query). "Text of your query/prompt." Generated using OpenAI. https://chat.openai.com/

Note that the assignments require discussing the original data sets that you generate in this course. Output from ChatGPT will not be able to discuss your dataset or interpret your graphs in a logical way.

Access and Accommodations

The University of Oregon and I are dedicated to fostering inclusive learning environments for all students and welcomes students with disabilities into all of the University's educational programs. The Accessible Education Center (AEC) assists students with disabilities in reducing campus-wide and classroom-related barriers. If you have or think you have a disability (https://aec.uoregon.edu/content/what-disability) and experience academic barriers, please contact the AEC to discuss appropriate accommodations or support. Visit 360 Oregon Hall or aec.uoregon.edu for more information. You can contact AEC at 541-346-1155 or via email at uoaec@uoregon.edu.

I am a designated reporter. For information about my reporting obligations as an employee, please see Employee Reporting Obligations on the Office of Investigations and Civil Rights Compliance (OICRC) website. Students experiencing sex- or gender-based discrimination, harassment or violence should call the 24-7 hotline 541-346-SAFE [7244] or visit safe.uoregon.edu for help. Students experiencing all forms of prohibited discrimination or harassment may contact the Dean of Students Office at 541-346-3216 or the non-confidential Title IX Coordinator/OICRC at 541-346-3123 to request information and resources. Students are not required to participate in an investigation to receive support, including requesting academic supportive measures. Additional resources are available at investigations.uoregon.edu/how-get-support. I am also a mandatory reporter of child abuse. Please find more information at Mandatory Reporting of Child Abuse and Neglect.

Pregnancy Modifications. Pregnant and parenting students are eligible for academic and work modifications related to pregnancy, childbirth, loss of pregnancy, termination of pregnancy, lactation, and related medical conditions. To request pregnancy-related modifications, students should complete the Request for Pregnancy Modifications form on the OICRC website. OICRC coordinates academic and other modifications for pregnant and parenting students to ensure students can continue to access their education and university programs and activities.

Accommodations for Religious Observances

The University of Oregon respects the right of all students to observe their religious holidays, and will make reasonable accommodations, upon request, for these observances. If you need to be absent from a class period this term because of a religious obligation or observance, please fill out the Student Religious Accommodation Request fillable PDF form and send it to me within the first weeks of the course so we can make arrangements in advance.

Course grading

• Two exams, each covering about 1/2 of the course and each worth 25% of your total grade.
• Five lab reports for a total of 50% of your grade, weighting of the grades will increase with expectations and complexity of the lab. Each assignment's instructions will include a grading rubric. Also, see the document on general notes for writing lab reports (on Canvas).
• The five laboratory topics roughly correspond with current lecture topics.  Most labs involve two meetings and involve the collection and interpretation of data.
  • The tree adaptations lab involves two walks around campus to observe traits of several tree tree species from throughout the world.  You are to create inventive hypotheses regarding the adaptive role of differences in related tree species. 5%
  • The virtual mega-transect lab meets during only one week and involves more independent work.  This involves comparing vegetation structure with climate variables across continental transects (using online resources). 10%
  • The spatial patterns lab addresses the distribution of individuals of a population, and is meant to demonstrate how certain processes leads to spatial patterns.  It also involves use of a statistical test to test hypotheses. 15%
  • The island biogeography lab uses a simulation of the processes that lead to species richness on an island.  Data collected during the first week are analyzed during the second week. 15%
  • The invasive species lab will consist of a film from Oregon Public Television.  Meeting on week 10 involves short presentations of a particular invasive species. The assignment will involve extra reading and thinking about invasive species. 5%. Lab 5 will be graded as credit/no credit: ALL questions must be answered to get credit!

Each lab will culminate in a lab report in which you are to answer specific questions. While it is helpful to discuss the labs amongst each other, and many labs are performed in groups, the lab reports are to be completed individually. Note the due dates for lab reports on the syllabus: lab reports are due at the lab meeting time. For each day late, grades will decrease by 10% of the total possible lab grade.

Read the lab before each lab meeting.

Required readings

• All readings will be supplied online through Canvas. You may wish to purchase the following book (no longer in print) if you can get a copy through Amazon or another seller:
  • Here Be Dragons, by Dennis McCarthy. Oxford University Press.
• Content of the lab sections will be on exams.
• Lab manuals and additional materials will be posted on canvas.uoregon.edu.

SCHEDULE

See Canvas Modules (one per week) to access the readings and lab materials. Bold indicates required readings. Italic indicates optional readings.

References for Readings

• Cox, C. B., R. Ladle, and P. D. Moore. 2016. Biogeography: An Ecological and Evolutionary Approach. John Wiley & Sons.
• Darwin, C. 1859. The Origin of Species. P. F. Collier & Son.
• Flannery, T. 2015. The Eternal Frontier: An Ecological History of North America and Its Peoples. Grove/Atlantic, Inc.
• Gavin, D. G. 2012. Biogeography. Pages 77-89 in J. P. Stoltman, editor. 21st Century Geography: A Reference Handbook. SAGE Publications, Thousand Oaks, CA.
• Jackson, S. T. 2004. Quaternary biogeography: Linking biotic responses to environmental variability across timescales. Pages 47-65 in M. V. Lomolino and L. R. Heaney, editors. Frontiers of Biogeography: New Directions in the Geography of Nature. Sinauer, Sunderland, MA.
• Lomolino, M. V., B. R. Riddle, J. H. Brown, and R. J. Whittaker. 2010. Biogeography. Fourth Edition. Sinauer Associates, Sunderland, MA.
• MacDonald, G. M. 2003. Biogeography: Space, Time and Life. Wiley, New York.
• McCarthy, D. 2011. Here Be Dragons: How the study of animal and plant distributions revolutionized our views of life and Earth. OUP Oxford.
• Molles, M. C. 1999. Ecology: Concepts and Applications. WCB/McGraw-Hill.
• Perry, D. A., R. Oren, and S. C. Hart. 2013. Forest Ecosystems. JHU Press.
• Pielou, E. C. 1974. Population and Community Ecology: Principles and Methods. Gordon and Breach.

• Interesting and potentially useful web links

Biogeography, once a secret delicacy enjoyed only by geniuses, must now be elevated from its current obscurity and placed alongside literature and history as an indispensable component of a truly enlightened education. —Dennis McCarthy, Here Be Dragons.