Dr. Linder: BIO 110A; 471-7825;
rlinder@mail.utexas.edu
Office
hours: Tues, 4-5:30 pm, BIO 110A or by arrangement
Meeting times: M 3-5, The
second meeting time is yet to be determined.
Total
class hours per week are 3-4.
Course web site: www.sbs.utexas.edu/bio386
Texts (All texts for this course are optional, I'll be providing what you need in pdf format, but please feel free to purchase any that you think would be useful at the book source of your choice. Below are texts that I have found useful.)
Books on the Comparative Method
Brooks and
McLennan. 1991. Phylogeny, Ecology, and Behavior. Chicago
University Press, Chicago.
Harvey, P.
H. and Pagel, M. D. 1991.
The Comparative Method in Evolutionary Biology.
Oxford University Press, Oxford.
Books on Phylogenetic Reconstruction
Hillis, D. M., Moritz, C., and
Mable, B. K. 1996.
Molecular Systematics, 2nd ed.
Sinauer Associates, Sunderland, MA.
Felsenstein, J. 2003. Inferring Phylogenies. Sinauer Associates, Sunderland, MA.
Overview
With the development of molecular tools and of modern methods for phylogenetic reconstruction, systematics has undergone a resurgence. New phylogenetic hypotheses based upon the data generated by the new technologies are widely available. The availability of well- or at least better-supported phylogenies has in turn led to a resurgence of the comparative method in biology, that is, the testing of evolutionary, ecological and behavioral hypotheses in an explicitly historical evolutionary context. It has also provided tools to reconsider whether patterns and processes operating at the microevolutionary level are sufficient to account for what is seen at the macroevolutionary level. The main goal of this course is to acquaint you with the theoretical underpinnings, methods, and significant contributions of the comparative method, an exciting, field of study.
Since this course is ultimately about inferring causation from the patterns generated by historical processes, we will begin by considering the history of the comparative method: its initial development, decline, and re-emergence. While this may at first appear a waste of time, I believe that knowledge of this history can help prevent us from reinventing the wheel or going down blind alleys by making us aware of what has gone before.
Because the comparative method must begin with a phylogeny, we will spend a bit of time on the evolutionary paradigm(s) and methods for generating a phylogeny. It is not my intention to turn this into a systematics methods course, but one must be aware of the theoretical assumptions and potential pitfalls associated with generating a phylogeny in order to have a deeper understanding of the results one can generate when testing comparative hypotheses. As with statistics, an understanding of the assumptions and methods can prevent you from making serious errors in the choice of methods and in the interpretation of your results.
Once we have covered phylogenetic reconstruction, we will examine the range of processes the comparative method can be used to test and we will learn some of the common methods in the field. The mantra of this section could easily be "Pattern and Process." By looking at patterns among organisms, we will attempt to infer the process(es) responsible for the patterns or at least falsify processes that are inconsistent with the pattern. This is an undertaking that is both exciting and fraught with potential pitfalls. We will cover both aspects. To do so will require an explicit understanding of the evolutionary and ecological paradigms/theories that underlie our ideas about the processes and an awareness of alternative processes that could generate the same patterns. Limitations of the comparative method will be considered, and we will discuss other methodologies that can be used in conjunction with the comparative method. We will also learn about the methodologies that have been developed to test comparative hypotheses and how they reflect the underlying ideas about evolution. Finally, you will learn about two or three (maybe even four) computer programs that are used to analyze comparative data and will have the opportunity to use them to analyze some data on your own.
Course Structure and Responsibilities. The course will have three parts that overlap and reinforce one another. Initially, there will be weekly assignments on various topics each consisting of a class section during which I give a “lecture” to familiarize you with the subject area and a class section during which a student leads a discussion on one or two papers from the primary literature. During my “lectures,” I encourage you to interrupt to ask for clarification or to amplify or disagree with something I’ve said. As long as you have made a sincere effort to read the assigned text before class, I will always be happy to entertain questions and comments from you. Later, we will revert almost entirely to a discussion format, with students being responsible for preparing and leading them. Second, there will be computer-based classes to familiarize you with some of the tools that are available for comparative analyses. Third, each of you will undertake a project in which you attempt to test a hypothesis using the comparative method. I address each of these parts in detail below.
Part 1: Lectures and discussion of texts and the primary literature.
Topics will usually be introduced by a lecture to help provide background and context. There will be assigned readings from your text or handouts for each of these topics. As the course progresses, I will lecture less and expect you to be prepared to discuss the readings. It is essential that you read the parts of the text assigned for a topic before you come to class. Don’t worry if you have questions or don’t understand everything on a topic before you come to class. All I ask is that you’ve made a good faith effort before you come to class. We can use your questions as jumping off points during the lecture or as indicators about the parts of the topic that we need to focus on more closely. Don’t be afraid to ask questions when you don’t understand. That fear is a much greater impediment to your learning than any trepidation you may feel about letting your fellow students (or me) know that you don’t understand something. I will not be judging you negatively if you do not completely understand all of the material before you enter the class. I have considerable respect for individuals who have the presence of mind to know that they do not completely understand a topic and who are willing to do what it takes to remedy that deficiency.
In addition to information from our texts, there will be readings from the primary literature and a discussion led by one of the students in the group. Each of you will sign up to lead one of these meetings. Leading a meeting will consist of three tasks.
1. You will be responsible for going through the primary literature on the topic and assembling a reference list that will be given to the other members of the class. This has a number of benefits, not the least of which is that each member of the class will have a reference list for the comparative method when the class is over. If you use EndNote (you really should start using some form of reference manager anyway), provide me with your reference list as an EndNote file and I will post it to the web.
2. From that reference list, you will assign one or two papers to be read and discussed by the class. This is going to require some preparation on your part. Papers should be assigned the week before the meeting when they will be discussed. And two weeks before the discussion you should come talk with me about what you plan to assign. You should have a sufficient number of copies of the assignment to hand out to the rest of the class (including me!), or a PDF version of the text, when you announce the assignment. I will post PDFs to the course web site.
3. You should be prepared to lead a discussion of the text and the papers. The key word here is "discussion." Most of us have a tendency to lecture on a topic (myself included) when we lead a class because that is what we are used to. My ideal for this class is to avoid that and to have the leader act as a facilitator of a real discussion among all the members of the class. This means that the leader should have a clear idea of what the key points in the paper(s) are before coming into class and should make sure that we cover those points, but that he or she should not feel compelled to demonstrate their mastery of the material. This is a difficult skill to develop, but worthwhile when working with intelligent colleagues (which you all are) who may approach a subject from a different point of view. I suggest you start with a brief (no more than about 15 min) overview of a paper and then open the topic up for discussion.
Part 2: Tutorials for
learning computer programs for comparative analysis.
There are a number of computer programs that can be used for comparative analyses. I want you to be aware of them, but we will concentrate on four during this course: MacClade, Mesquite, CAIC (Comparative Analysis by Independent Contrasts), and CACTUS. MacClade is an excellent program for interactively exploring and testing hypotheses about the evolution of discrete characters. However, it has limited capacity for analyzing quantitative/continuous characters. Mesquite is an open source program, freely available on the web. It is very powerful and does much more than just comparative analyses. However its power also makes it somewhat difficult to use. I'm going to try to at least get you comfortable enough with the program so you can use it beyond the class. CAIC is a Mac implementation of methods developed for analyzing continuous characters and CACTUS is an IBM/PC program for doing much the same. They’re not as slick as MacClade, but they do allow one to work with quantitative traits. I have set aside at least four class meetings for familiarizing you with the programs. If there is time we may look at some other programs, such as COMPARE.
Part 3: Projects to test a hypothesis using the comparative method.
When it comes to data analysis, most of us learn best by doing, so each of you will undertake a project using the comparative method. This analysis can take many forms. If you are far enough with your own research, you could analyze your own data. I encourage this, no matter how preliminary or unsophisticated it might be, because we always take a greater interest in things that are important to us. If you do not have your own data set, you should work with a data set from the literature, preferably on a topic that interests you. Many authors are now making their data sets available through archives or on request so it shouldn’t be too difficult. We will have a series of presentations of persons’ analyses at the end of the semester. Don’t wait until the last minute to start working on your project! To make this easier, I will meet with each of you before September is over to discuss your project idea(s).
Finally, you may have certain areas that are of particular interest to you. Please feel free to talk with me about your ideas at any time during the course and we’ll see if we can introduce additional material on those topics.