ANALYSIS OF DNA-SEQUENCE DATA - PHYLOGENETIC INFERENCE

The chapter discusses phylogenetic inference for the analysis of DNA sequence data. There are five basic steps in the phylogenetic analysis of DNA sequences. The sequences under study must first be aligned so that positional homologs (the units of comparison) may be analyzed. Alignment may be straightforward if pairwise differences are small and most differences result from substitutions but it becomes increasingly difficult as the sequences become more divergent and insertion/deletion events become more common. Once sequences are aligned, some assessment of the presence of phylogenetic signal is necessary. If phylogenetic signal is present in a matrix of sequences, then the third step is selecting a method of phylogenetic inference. Once a method has been selected and the appropriate software has been obtained, a strategy must be developed for finding the best tree under the selected optimality criterion. Once a tree has been obtained, some statement of confidence in the results is desirable, such as deciding which nodes of the tree are well-supported by the data, and which are not. © 1993, Elsevier Inc. All rights reserved.