Recent studies based on different types of data (i.e., morphology, molecules) have found strongly conflicting phylogenies for the genera of iguanid lizards but have been unable to explain the basis for this incongruence. We reanalyze published data from morphology and from the mitochondrial ND4, cytochrome b, 12S, and 16S genes to explore the sources of incongruence and resolve these conflicts. Much of the incongruence centers on the genus Cyclura, which is the sister taxon of Iguana, according to parsimony analyses of the morphology and the ribosomal genes, but is the sister taxon of all other Iguanini, according to the protein-coding genes. Maximum likelihood analyses show that there has been an increase in the rate of nucleotide substitution in Cyclura in the two protein-coding genes (ND4 and cytochrome b), although this increase is not as clear when parsimony is used to estimate branch lengths. Parametric simulations suggest that Cyclura may be misplaced by the protein-coding genes as a result of long-branch attraction; even when Cyclura and Iguana are sister taxa in a simulated phylogeny, Cyclura is still placed as the basal member of the Iguanini by parsimony analysis in 55% of the replicates. A similar long-branch attraction problem may also exist in the morphological data with regard to the placement of Sauromalus with the Galápagos iguanas (Amblyrhynchus and Conolophus). The results have many implications for the analysis of diverse data sets, the impact of long branches on parsimony and likelihood methods, and the use of certain protein-coding genes in phylogeny reconstruction.
