Molecular phylogenetics of the Muscidae (Diptera:Calyptratae): new ideas in a congruence context

Abstract

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.

Say goodbye to tribes in the new house fly classification: A new molecular phylogenetic analysis and an updated biogeographical narrative for the Muscidae (Diptera)

“…This clade is strongly supported in all analyses through Bayesian inference (here we consider bootstrap ≥ 70% and posterior probability ≥ 95% to indicate strong support). The close relationship between Muscini, Stomoxyini and Azeliini (Azeliinae) has already been noted in other molecular phylogenies (Schuehli et al 2007, Kutty et al 2008, 2010. The relationship between these and Achanthipterinae was also found by Kutty et al (2014).…”

“…1). This lineage is not strongly supported in most analyses (incompletely recovered in five), but the affinity between the Reinwardtiini and Cyrtoneurininae has already been demonstrated in other molecular (Schuehli et al 2007, Soares 2008) and morphological studies (Skidmore 1985).…”

“…We used the mitochondrial cytochrome c oxidase subunit I gene (CO1), and the nuclear genes aspartyl-tRNA synthetase (AATS), region 4 of carbamoylphosphate synthetase-aspartate transcarbamoylase-dihydroorotase (CAD), and elongation factor 1-α (EF1-α). All genes are among the most commonly used for Diptera phylogeny (Gibson et al 9 2011) and have been used in studies of the Muscidae (e.g., Kutty et al 2008, 2010, Schuehli et al 2007, Wiegmann et al 2011). Primer sequences for the genes used for Polymerase Chain Reaction (PCR) are listed in Supplementary Table 2. Focusing on intergeneric relationships, we did not amplify these genes for all species, but rather used one species per genus (the type-species, when available) in which we amplified all genes.…”

“…The first molecular phylogenetic study of the Muscidae examined 24 terminal groups in five subfamilies based on the following four genes: CO1, CO2, EF1-α and CAD (Schuehli et al 2007). That study only found monophyly of two subfamilies, Muscinae and Phaoniinae.…”

Carcases and mites

“…Species in the genus Ophyria have meanwhile been transferred to the genus Hydrotaea, however, molecular studies place Ophyria species in a clade separate from Hydrotaea (Schnell e Schühli et al 2004Schühli et al , 2007. The bottle must have been part of original material offered to the museum by Mégnin.…”