Partitioning of Multiple Data, Sets Phylogenetic Analysis

This chapter deals with the methodological aspects involved in phylogenetic analysis of multiple data sets within a maximum parsimony framework. Comparisons of character sets within a maximum likelihood paradigm are discussed elsewhere [1-6]. Below, we (1) review the three basic philosophies of data partitioning and combination in phylogenetic analysis (2) present some analytical methods available for examining the distribution of support and conflict among data sets in a combined analysis framework (3) use two empirical examples to illustrate different approaches to partitioned and combined phylogenetic analyses and (4) review the methodology required to perform some of these analyses using PAUP* [7] and ARNIE [8].