Molecular phylogeny of the Drosophila auraria species complex and allied species of Japan based on nuclear and mitochondrial DNA sequences

We studied the phylogenetic relationships among the six species of the Drosophila auraria species complex and three species of the montium species subgroup endemic to Japan. To do this, we examined the DNA sequences of the nuclear ITS1 and the mitochondrial COII of these species. Intraspecific variation in ITS1 was observed for most of the species studied. However, interspecific variation was small and of the same magnitude as intraspecific variation among D. auraria, D. triauraria, and D. quadraria. In addition, the amount of intraspecific variation between COII sequences from D. auraria and D. triauraria was almost the same as that of the interspecific variation between these species. Phylogenetic trees based on ITS1 or COII data reveal that, with the exception of D. pectinifera, these species can be separated into two taxonomic groups. D. rufa formed a taxonomic lineage with two Japanese endemic species, D. asahinai and D. lacteicornis. Physiological and behavioral differences between D. auraria and D. triauraria have been reported, but our results differed from those previously reported. Such differences may be better explained by hybridization between D. auraria and D. triauraria than by similarity due to recent common ancestry. Both the ITS1- and COII-based phylogenetic trees placed D. pectinifera outside the auraria complex. However, D. pectinifera sequences were more similar to those of the auraria complex than those of D. punjabiensis, another species thought to be closely related to members of the auraria complex.