Introduction

 
This course is for graduates or advanced undergraduates who wish to learn about biological systematics with particular reference to molecular character evolution and phylogeny reconstruction. Biological Systematics will cover the theory of systematics, character evaluation and homology assessment, molecular data types, methods of phylogeny reconstruction, optimality criteria, tree evaluation and comparison, and the use of phylogenies in comparative biology.
 
 
The comparative method has assumed a central role in evolutionary biology but is predicated on accurate and resolved phylogenies. Traditional systematics is largely based on intuitive notions of evolutionary process, relatively subjective delimitations of species, and comparatively crude methods of analysis. Most of this is due to reliance on "phenotypic" characters and the patterns of variation they exhibit. The large amount of molecular data that is currently being generated has forced a re-evaluation of both the nature of character data and the methods of data analysis. To foster an appreciation of the prospects and limitations of comparative biology, Biological Systematics will provide a clear description of the purpose and goals of systematics, elaborate on the nature of molecular systematic data, and examine the mechanics of phylogenetic analysis. The course will use a wide range of computing resources and software options for analysis of evolutionary and systematic data.
 
 
The course will consist of one hour of lecture and one hour of computer lab or discussion per week. Over the semester, four general topics will be considered. First, a relatively short introduction to the nature of phylogenetic studies will be presented emphasizing the methods and approaches common to the study of different groups of organisms (e.g., plants, insects, mammals, fungi, etc.) and an overview of the different types of data used in phylogenetic studies (e.g., morphological, molecular, etc.). The lab sessions associated with this section will entail a presentation of Internet resources pertinent to phylogenetics (such as museum databases, the Tree of Life, and TreeBase) as well as an introduction to character analysis software (such as MacClade). The second section of the course will be a thorough discussion of character data as it pertains to phylogenetics. The lab component will include online molecular data resources (such as GenBank and NCBI's Entrez), sequence alignment tools (such as CLUSTAL) and sequence analysis software (such as Sequencher, the ABI collection, and GCG via the Internet). The third section of the course will cover phylogenetic analysis including parsimony, distance, and maximum likelihood-based approaches. The computer component of this section will involve use of many different pieces of software including PAUP*, PHYLIP, and MEGA. The fourth and final section of the course will demonstrate the applications of phylogenetics in the study of character evolution, biogeography, coevolution, molecular evolution, and conservation biology. The computer sessions will demonstrate different approaches to the use of phylogenies in a graphical environment (such as COMPONENT and TreeMap).