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    Molecular Ecology

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    Spring 2016


    Tuesday/Thursday 930-1045, Ecology Conference Room

    This class is fundamentally about ecology - the study of the distribution and abundance of organisms - while recognizing that much of biodiversity can only be accurately described based on genetic/molecular data. These data allow us to separate populations that may have very different ecological and evolutionary dynamics (in some cases, while having the same Latin binomial species name); understand how demography influences the diversity of a population; and track the presence or distribution of things we cannot see (pathogens, microbes, or other organisms that are hard to locate or count).

    We will discuss a lot of genetic information at first - marker types, models of evolution, and means of collecting data. Then, our analytical focus will turn to addressing the kinds of questions many of you are interested in answering. For many of the lectures and exercises, it will be assumed that you have read some background material from the text chosen for this class. In addition, you will have readings from this edited book on diversity statistics. Please support local booksellers when possible, or get the e-book to save resources as appropriate.

    Syllabus

    The syllabus is a general plan for the course. Deviations announced to the class by the instructor may be necessary. OK, that is out of the way, here is the basic blueprint for our semester. All of this, of course, falls under your agreement to abide by UGA's "Culture of Honesty".


    Each week (well, most weeks) we will read and a team of class members will present a paper from the literature. The goal is to make sure we understand the rationale for molecular exploration of this system, the implications of the results, and the methods well enough that we can turn around and apply them to our own projects.

    Additionally, we will explore some very basic molecular ecology analysis of our own. This year, most of this will be in terms of pre-selected exercises from your text and from a series of exercises in R to learn how to apply these inferences.

    Students are strongly encouraged to work in R, but other packages such as GenAlEx, Arlequin, DNAsp and others may be of use as well.

    Tools

    I bet we will find this haplotype diversity simulator of use early on!

    For visualizing the coalescent process...

    To learn more about coalescent theory, start with this paper:

    Download file "coalnrg.pdf"

    Beyond that I highly recommend Wakeley's 2008 book on coalescent theory, and I may teach a 1-credit course using that book in Fall 2016 if there is sufficient interest. Let me know.


    Evaluation

    Students will be evaluated in this course through:

    1. Attendance and participation (25%) Attendance is binary, you are either there or not, and I'll keep track. Participation is hard to mandate or regulate but we will be using a "blackjack" system where your contribution to class in Discussion or during lecture (asking a legit question, etc.) gets you a playing card. Once you have 3 cards, you can only get a new one by helping LEAD the discussion by addressing new questions to your colleagues or taking us in a good new direction. At the end of appropriate class sessions I'll ask for your score in blackjack, higher scores are better but you don't want to go over 21! No, your end score will not be your actual score for the day but it gives you and I an indication of how well you are participating, and encourages people who are comfortable with talking and contributing to know when they have done enough and need to help bring in others to the conversation.


    2. Wikipedia Project (20%) The first ~6 weeks of the semester you will be working in small groups to learn molecular models of evolution, and to ensure you think hard about the differences in these models and how they are applied you will be contributing entries to Wikipedia. More details on the first day of class. This assignment is about quality of thought and writing as well as your ability to work with others.

    3. Exercises (20%). Each week there will be considerable amount of out-of-class reading and exercises. Please keep up! These will not just pertain to discussions but to support the limited amount of time we have for passive lecture/listen. In addition to the reading, there are exercises both in the Freeland text as well as to be completed in R to gain experience with some methods. In these cases, you will submit a one-page summary of your exercise and what you found, how it will be applicable to your research, etc.

    4. Proposal (35%). The latter half of the semester you will integrate much of what you have learned with your own research interests and develop a 10-page proposal (including references, tables, and figures). These will be peer-reviewed at least once prior to turning in for grading. The criteria for grading include the clarity of writing (25%), novelty and appropriate concepts and methods (25%), excellent scholarship and support for your ideas and arguments (e.g. references, 25%), and the detail and thought that goes into the 1-page (max) budget (25%). Again, this written assignment will be evaluated once by Dr. Wares for content, ideas, and quality of communication; once by peers to improve on this draft; and a final version that is graded.