Molecular phylogeny of Allodia (Diptera: Mycetophilidae) constructed using genome skimming

In this study, we use low-coverage shotgun sequencing of genomic DNA, commonly referred to as genome skimming, to investigate the phylogenetic relationships of the fungus gnat genus Allodia Winnertz (Mycetophilidae, Mycetophilinae, Exechiini). Nineteen specimens, representing 16 in-group and three outgroup taxa, were successfully sequenced and molecular markers of both mitochondrial and nuclear origin were retrieved. The phylogenetic analyses of 13 protein-coding mitochondrial genes, two ribosomal mitochondrial genes and the nuclear ribosomal 18S and 28S strongly support the monophyly of its two subgenera Allodia s.s. and Brachycampta. Complete mitochondrial genomes of 15 species were assembled, which enables further comparisons with the mitochondrial genomes of other Diptera. Overall, the methodology used in this study proved successful and promising for other dipteran groups. In addition to the phylogenetic reconstruction, the morphological characters previously used to separate the two subgenera were evaluated and re-examined. Together with the composite structure of the male genitalia, we consider details of the scutal bristles appropriate for separating the two groups. Based on the achieved results, we reinstate Brachycampta stat. rev. as a separate genus.