Resolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling
The debate about whether phylogenetic accuracy is most efficiently increased by sampling more characters or more taxa is certainly not new (e.g., Kim, 1996; Graybeal, 1998; Poe, 1998a, b; Rannala et al., 1998; Poe and Swofford, 1999; Pollock and Bruno, 2000; Rosenburg and Kumar, 2001; Pollock et al., 2002; Zwickl and Hillis, 2002; Rosenberg and Kumar, 2003; Hillis et al., 2003). However, the recent increase of whole genomic sequences available from an assortment of distantly related taxa makes this debate highly relevant to researchers across fields of biology. Recently, Rokas et al. (2003) argued that the true species tree can be recovered despite conflicting phylogenetic signal between genes if enough genes are used in the analysis. Using the bootstrap proportion (BP) as a measure of phylogenetic accuracy, they concluded that approximately 20 genes are needed to ensure a robustly supported tree (> 95% BP) for their study group of eight yeast taxa. From these empirical results, they generalized that most molecular phylogenetic studies have probably included insufficient numbers of genes to confidently resolve relationships within their respective focal groups.