Character congruence and phylogenetic signal in molecular and morphological data sets: A case study in the living iguanas (Squamata, Iguanidae)

The lizard family Iguanidae comprises eight living genera distributed throughout the New and Old World, and includes several island endemics. We reconstruct phylogenetic relationships among these genera using 90 previously published morphological characters, to which we add a molecular (mtDNA sequence) data set that includes 742 nucleotides of the ND4 gene and the complete sequences of the histidine, serine, and leucine tRNAs (217 nucleotides). Trees were initially constructed separately from these three data sets, and then tested for significant conflict in topologies that would suggest the influence of different evolutionary processes. The three data sets were then combined, and a single tree was obtained from the total evidence that permitted identification of potential sources of character incongruence. Several additional analyses of the combined data sets were repeated with sequential deletion of successive classes of homoplastic characters, and we show that the same single tree topology is recovered in most cases. However, part of the tree structure collapses when the matrix of combined characters is completely purged of all homoplastic characters. We argue that this extreme results in an unacceptable loss of phylogenetic information, and we present a single phylogenetic hypothesis for all living genera of iguanas. We show that this hypothesis is significantly more parsimonious than either of two previously published trees, and we discuss the evolution and biogeography of the Iguanidae based on the preferred hypothesis.