War of the iguanas: Conflicting molecular and morphological phylogenies and long-branch attraction in iguanid lizards

Recent studies based on different types of data (i.e., morphology, molecule s) have found strongly conflicting phylogenies for the genera of iguanid li zards but have been unable to explain the basis for this incongruence. We r eanalyze published data from morphology and from the mitochondrial ND4, cyt ochrome b, 12S, and 16S genes to explore the sources of incongruence and re solve these conflicts. Much of the incongruence centers on the genus Cyclur a, 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 othe r Iguanini, according to the protein-coding genes. Maximum likelihood analy ses show that there has been an increase in the rate of nucleotide substitu tion in Cyclura in the two protein-coding genes (ND4 and cytochrome b), alt hough this increase is not as clear when parsimony is used to estimate bran ch 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 sti ll 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 t he Galapagos iguanas (Amblyrhynchus and Conolophus). The results have many implications for the analysis of diverse data sets, the impact of long bran ches on parsimony and likelihood methods, and the use of certain protein-co ding genes in phylogeny reconstruction.