In many organisms, gene trees based on nuclear mark ers and those based on cytoplasmic markers (chloroplasts or mitochondria) sometimes indicate quite different re lationships among the species being studied (e.g., Rieseberg and Soltis 1991; Rieseberg et al. 1996; Cathey et al. 1998; Bergthorsson et al. 2003; Avise 2004; Croucher et al. 2004; Sullivan et al. 2004; Chan and Levin 2005; Fehrer et al. 2007; Linnen and Farrell 2007). This in congruence is normally attributed to incomplete lineage sorting (when two al?eles coalesce prior to speciation and do not track the species phylogeny), introgression (interspecific hybridization followed by unidirectional backcrossing), horizontal gene transfer, or errors in phy logenetic reconstruction. Although the usual explanations for cytoplasmic nuclear incongruence are well documented, these expla nations are often assumed rather than demonstrated in