Are mitochondrial genes useful for the analysis of monocot relationships?

The plastid genome, as sampled by nucleotide sequencing of genes and other regions, has been used more extensively than any other genome in the study of plant phylogenetic relationships (e.g., Palmer & al., 2004; and associated review articles). Although the major initial thrust of these studies was in the area of higher-level relationships (generally at the level of the genus and above), predominantly using rbcL and other protein-encoding genes of the plastid genome, many studies also have utilized noncoding regions of the plastid genome, usually for the analysis of lower-level relationships (e.g., Shaw & al., 2005; and citations within). More than a decade ago, Palmer (1992) discussed the potential utility of mitochondrial genes for plant phylogenetic purposes, but in the intervening period this genome has been used relatively infrequently, while the use of low-copy-number nuclear genes, which was rare at that time, has increased dramatically. This is not to say that mitochondrial genes have been ignored. The utility of mitochondrial genes for phylogenetic studies of achlorophyllous plants has been demonstrated in groups such as the Rafflesiales (Nickrent & al., 2004), and multigene studies often include one or more mitochondrial genes (e.g., Qiu & al., 2006). The literature on the use of mitochondrial DNA in plant systematics, and on challenges associated with its use (such as RNA editing), are reviewed elsewhere in this symposium (Petersen & al., 2006; Qiu & al., 2006), and readers are referred to those contributions for further information. In the present paper we examine the contribution of individual mitochondrial genes to the support of particular clades, in the context of a multi-gene analysis that also includes widely used genes of the plastid genome, with the goal of determining whether the mitochondrial genes contribute significantly to the results. Further, if they do contribute significantly, it is useful to determine whether this contribution takes the form of generalized support or opposition to the relationships supported by the plastid genome, or is a mixture of these two. The power and utility of various genes and other character sets for phylogenetic analysis are difficult to assess, in part because true historical descent relationships among the terminals (i.e., the taxa) are not known for real data matrices of nontrivial size and complexity. Are mitochondrial genes useful for the analysis of monocot relationships?