The muscid genus Ophyra has long been the subject of debate over its placement within the family. However, a phylogenetic study has never been conducted that would clarify its systematic position. In the present paper, phylogenetic relationships are examined between Ophyra albuquerquei and related muscid genera. The mitochondrial genes Cytochrome Oxidase I and II and tRNA-Leu were used combined with the nuclear genes CAD and Elongation Factor 1 to compose a matrix with 2989 characters (716 parsimonyinformative). These characters were analyzed under parsimony resulting in a single most parsimonious tree. Contrary to some recent classifications, our molecular data suggest the placement of Ophyra albuquerquei within the Muscinae in a separate position from the azeliine genus Hydrotaea.

Hypotheses about the evolution of Muscidae have long been the subject of continuous re-evaluation and reinterpretation. Current understandings of the relationships among these flies are based mainly on a single set of characters and are therefore questionable. Our understanding of muscid phylogeny thus needs greater support and further corroboration from additional suites of characters. In the current study, we analysed phylogenetic relationships among 24 species of muscid flies (18 genera and six subfamilies) using 2989 characters derived from sequences of mitochondrial (COI and COII) and nuclear genes (CAD and EF-1α). Data from each gene partition were analysed both in combined and separate phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian inference. Support was found for the monophyly of the Muscidae in all analyses and for a sister-group relationship between Coenosiini and Phaoniinae. The latter group was placed in a clade with sampled species of Reinwardtiini and Cyrtoneurininae. The genera Ophyra and Hydrotaea were placed in the Muscinae and a sister-group relationship for Musca and Stomoxys was supported. Sampled species of Polietina form a monophyletic lineage, while Morellia was found to be paraphyletic. Combined analysis of gene partitions improved support and resolution for resulting topologies despite significant incongruence between data partitions found through application of the Incongruence Length Difference test.

Pseudoptilolepis Snyder, 1949, a monophyletic Neotropical muscid genus of six species, is reviewed to include four new species, P. centralis sp. nov., P. chrysella sp. nov., P. crocina sp. nov. and P. elbida sp. nov. A taxonomic key is provided for the genus. The phylogenetic relationship among the studied species is: (P. centralis ((P. chrysella (P. fluminensis, P. fulvapoda)) (P. nudapleura (P. elbida (P. nigripoda, P. crocina))))). The geographic distribution of the species is also presented and briefly discussed.