Assessing Congruence: Empirical Examples from Molecular Data

Abstract

Numerous DNA regions representing the nuclear and both organellar genomes are now available for comparative sequencing in plants (see Chapter 1); in addition, morphological and chemical data can also be obtained for phylogenetic analyses. With such a diversity of potential data sets available and the relative ease with which DNA sequences can be obtained, the acquisition of multiple data sets for the same suite of taxa is straightforward. As a result, the number of groups for which multiple data sets is available is increasing rapidly. Although it is readily apparent that multiple data sets are needed for estimating phylogenetic relationships reliably, it is also recognized that different genes may, in fact, possess different branching histories (see Chapter 10). Consequently, incorporating multiple data sets into phylogenetic studies is not a casual undertaking. Essential tasks in the analysis of multiple data sets include assessing congruence between different phylogenetic trees and data sets, and ascertaining whether multiple data sets should be combined into a single data matrix prior to phylogenetic reconstruction.