PHYLOGENETIC ANALYSIS OF RESTRICTION SITE DATA

This chapter reviews different methods for the phylogenetic analysis of restriction site variation. It illustrates how these methods can be used by applying them to restriction site variation among genera within a subtribe of the sunflower family. Restriction fragment patterns can be characterized either as a simple list of fragment lengths or as mapped restriction sites. When comparing closely related taxa with a low level of sequence divergence, it may be possible to infer restriction site mutations by inspecting fragment profiles. This approach has been used successfully in restriction enzyme studies of chloroplast DNA at the inter- and intraspecific levels, where sequence divergence is in the range of 0.5–1.0%. Restriction fragment differences can be the result either of nucleotide substitutions in the recognition sequences or of length mutations. Restriction site variation has several characteristics that make it particularly appropriate for phylogenetic reconstruction: (1) character states can be scored unambiguously, (2) a large number of characters can be scored in each individual, and (3) it provides information on both the extent and the nature of divergence between two sequences. © 1993, Elsevier Inc. All rights reserved.