Choosing an Approach and an Appropriate Gene for Phylogenetic Analysis

A diverse array of molecular approaches is now available to the plant systematist for use in phylogenetic inference, including restriction site analysis, comparative sequencing, analysis of DNA rearrangements (e.g., inversions) and gene and intron loss, and various PCR-based techniques. Although these various methodologies present systematists with unparalleled opportunities for elucidating relationships and evolutionary processes, the sheer number of molecular approaches available, as well as the number of proven DNA regions for use in comparative sequencing, may seem overwhelming to those new to the field of molecular systematics. This chapter provides a general review of the various molecular techniques currently available to the plant systematist. Our primary goal is to review the types of molecular data sets that can presently be obtained; we discuss the advantages and disadvantages of each and the most appropriate approach for studying a given taxonomic level or type of evolutionary question. Given the current emphasis on DNA sequence data for phylogeny estimation, we then concentrate on the choice of an appropriate gene for comparative sequencing and also briefly discuss the pros and cons of manual versus automated sequencing. A description of selected PCR- mediated techniques for systematic and population-level studies is presented in Chapter 2.