Taxonomic boundaries, phylogenetic relationships and biogeography of the Drosophila willistoni subgroup (Diptera: Drosophilidae)

The Drosophila willistoni subgroup represents a complex with varying taxonomic levels. It encompasses D. willistoni and its five sibling species: D. equinoxialis, D. insularis, D. paulistorum, D. pavlovskiana and D. tropicalis. Of these, D. equinoxialis, D. tropicalis and D. willistoni present differentiation at subspecific level, whereas D. paulistorum represents a superspecies, formed by six semispecies. Despite this taxonomic and evolutionary complexity, many of these semi and subspecific taxa have not yet had their phylogenetic status tested in an explicitly molecular study. Aiming to contribute to the understanding of the evolution of this challenging group, we analyzed nucleotide sequences from two mitochondrial and four nuclear datasets, both individually and simultaneously, through different phylogenetic methods. High levels of incongruence were detected among partitions, especially concerning the mitochondrial sequences. As this incongruence was found to be statistically significant and robust to the use of different models and approaches, and basically restricted to mitochondrial loci, we suggest that it may stem mainly from hybridization-mediated asymmetrical introgression. Despite this, our nuclear data finally led to a phylogenetic hypothesis which further refines several aspects related to the willistoni subgroup phylogeny. In this respect, D. insularis, D. tropicalis, D. willistoni and D. equinoxialis successively branched off from the willistoni subgroup main stem, which recently subdivided to produce D. paulistorum and D. pavlovskiana. As regards the semispecies evolution, we found evidence of a recent diversification, which highly influenced the obtained results due to the associated small levels of genetic differentiation, further worsened by the possibly associated incompletely sorted ancestral polymorphisms and by the possibility of introgression. This study also raises the question of whether these semispecies are monophyletic at all. This reasoning is particularly interesting when one considers that similar levels of reproductive isolation could be attained through infection with different Wolbachia strains.