Problems with data quality in the reconstruction of evolutionary relationships in the Drosophila melanogaster species group : comments on Yang et al. (2012)

Letter to the editor: Yang et al. (2012) propose a phylogeny of the Drosophila melanogaster species group based on what is presented as a 100% complete data matrix of 17 genes, representing 48 species. The phylogeny presented in the publication provides strong support for a hypothesis regarding the evolutionary relationships of the melanogaster species group, and the importance of new data in reconstructing the phylogeny. However, an investigation of these data reveals some troubling issues with the identity and appropriateness of many of the sequences. These issues cast doubt on the published topology and reported maximum likelihood bootstrap values and Bayesian posterior probabilities, as well as the role the authors attribute to increased data matrices in reconstructing these phylogenetic relationships. In total, we found problems with 19% of the 816 sequences referenced in this study.