Testing heterogeneous base composition as potential cause for conflicting phylogenetic signal between mitochondrial and nuclear DNA in the land snail genus <Emphasis Type="Italic">Theba</Emphasis> Risso 1826 (Gastropoda: Stylommatophora: Helicoidea)

Several pitfalls can mislead phylogenetic analyses based on molecular data, including heterogeneous base composition. Previous work has revealed conflicting topologies in analyses of the land snail genus Theba Risso 1826 based on mitochondrial cytochrome oxidase subunit I (COI) and nuclear AFLP data, respectively. However, the third codon positions of COI had heterogeneous base composition, prompting the present investigation asking specifically if this was the cause for the mito-nuclear discordance. For a potentially better resolution of the mitochondrial data, we also sequenced a fragment of 16S rRNA, the loop sections of which proved to have inhomogeneous base frequencies as well. In partitioned phylogenetic analyses, we compared topologies generated from the original data to those based on alignments in which the heterogeneous partitions were RY-coded and to a LogDet transformed distance analysis. In addition, we tested whether conventional Bayesian analyses would reconstruct the original topology from inhomogeneous data simulated based on this original topology. All our analyses, regardless of whether we accounted for heterogeneous base frequencies or not, revealed very similar topologies, confirming previous findings. Thus, the phylogenetic signal of mtDNA in the land snail genus Theba appeared to be robust despite considerable inhomogeneity of base composition. Therefore, the discordance of mitochondrial and nuclear topologies is probably real and most likely a consequence of incomplete lineage sorting.