Phylogenetic utility of different types of molecular data used to infer evolutionary relationships among stalk-eyed flies (Diopsidae)

A phylogenetic hypothesis of relationships among 33 species of stalk-eyed f lies was generated from a molecular data set comprising three mitochondrial and three nuclear gene regions. A combined analysis of all the data equall y weighted produced a single most-parsimonious cladogram with relatively st rong support at the majority of nodes. The phylogenetic utility of differen t classes of molecular data was also examined. In particular, using a numbe r of different measures of utility in both a combined and separate analysis framework, we focused on the distinction between mitochondrial and nuclear genes and between faster-evolving characters and slower-evolving character s. For the first comparison, by nearly any measure of utility, the nuclear genes are substantially more informative for resolving diopsid relationship s than are the mitochondrial genes. The nuclear genes exhibit less homoplas y, are less incongruent with one another and with the combined data, ana co ntribute more support to the combined analysis topology than do the mitocho ndrial genes. Results from the second comparison however, provide little ev idence of a clear difference in utility. Despite indications of rapid diver gence and saturation, faster-evolving characters in both the nuclear and mi tochondrial data sets still provide substantial phylogenetic signal. In gen eral, inclusion of the more rapidly evolving data consistently improves the congruence among partitions.