A supermatrix-based molecular phylogeny of the family Drosophilidae

Abstract

SummaryThe genusDrosophilais diverse and heterogeneous and contains a large number of easy-to-rear species, so it is an attractive subject for comparative studies. The ability to perform such studies is currently compromised by the lack of a comprehensive phylogeny forDrosophilaand related genera. The genusDrosophilaas currently defined is known to be paraphyletic with respect to several other genera, but considerable uncertainty remains about other aspects of the phylogeny. Here, we estimate a phylogeny for 176 drosophilid (12 genera) and four non-drosophilid species, using gene sequences for up to 13 different genes per species (average: 4333 bp, five genes per species). This is the most extensive set of molecular data on drosophilids yet analysed. Phylogenetic analyses were conducted with maximum-likelihood (ML) and Bayesian approaches. Our analysis confirms that the genusDrosophilais paraphyletic with 100% support in the Bayesian analysis and 90% bootstrap support in the ML analysis. The subgenusSophophora, which includesDrosophila melanogaster, is the sister clade of all the other subgenera as well as of most species of six other genera. This sister clade contains two large, well-supported subclades. The first subclade contains the HawaiianDrosophila, the genusScaptomyza, and thevirilis-repletaradiation. The second contains theimmigrans-tripunctataradiation as well as the generaHirtodrosophila(exceptHirtodrosophila duncani),Mycodrosophila,ZaprionusandLiodrosophila. We argue that these results support a taxonomic revision of the genusDrosophila.