First molecular phylogeny of Paralucilia Brauer & Bergenstamm, 1891 (Insecta, Diptera, Calliphoridae): A preliminary approach.

Paralucilia Brauer & Bergenstamm, 1891 (Diptera, Oestroidea, Calliphoridae) is a small genus of blowflies restricted to the Neotropical region, which is commonly reported on decaying corpses and vertebrate carcasses. The number of species currently assigned to this genus and their denominations are contentious, with either three or five species recognized by different authors. This taxonomic instability results in a lack of consensus in species determination, making it impossible to compare results from different studies as well as to elaborate confident taxonomic keys. In order to solve some of the most commonly reported taxonomic conflicts within this genus, to the best of our knowledge, this study presents the first phylogenetic hypothesis for the relationships among Paralucilia species, based on molecular analysis of the COI, ITS2, 28S, and 16S genes. Maximum parsimony, maximum likelihood, and Bayesian inference analyses were used for phylogenetic reconstruction and divergence time estimation analyses. Intra- and interspecific genetic distances were calculated among species using the COI dataset. The results showed that at least three of the five currently accepted species are well defined: P. fulvinota, P. pseudolyrcea, and P. paraensis, however, a significant level of intraspecific variation was observed in P. fulvinota. These findings will assist future revisions of the description, classification, and distribution of species of Paralucilia, as well as in the elaboration of taxonomic keys. Additionally, we show that it is possible to clarify the evolutionary history of this Neotropical genus using supplementary evidence such as morphology and molecular data.

Phylogenomic analysis of Calyptratae: resolving the phylogenetic relationships within a major radiation of Diptera.

The Calyptratae, one of the most species-rich fly clades, only originated and diversified after the Cretaceous-Palaeogene extinction event and yet exhibit high species diversity and a diverse array of life history strategies including predation, phytophagy, saprophagy, haematophagy and parasitism. We present the first phylogenomic analysis of calyptrate relationships. The analysis is based on 40 species representing all calyptrate families and on nucleotide and amino acid data for 1456 single-copy protein-coding genes obtained from shotgun sequencing of transcriptomes. Topologies are overall well resolved, robust and largely congruent across trees obtained with different approaches (maximum parsimony, maximum likelihood, coalescent-based species tree, four-cluster likelihood mapping). Many nodes have 100% bootstrap and jackknife support, but the true support varies by more than one order of magnitude [Bremer support from 3 to 3427; random addition concatenation analysis (RADICAL) gene concatenation size from 10 to 1456]. Analyses of a Dayhoff-6 recoded amino acid dataset also support the robustness of many clades. The backbone topology Hippoboscoidea+(Fanniidae+(Muscidae+((Anthomyiidae-Scathophagidae)+Oestroidea))) is strongly supported and most families are monophyletic (exceptions: Anthomyiidae and Calliphoridae). The monotypic Ulurumyiidae is either alone or together with Mesembrinellidae as the sister group to the rest of Oestroidea. The Sarcophagidae are sister to Mystacinobiidae+Oestridae. Polleniinae emerge as sister group to Tachinidae and the monophyly of the clade Calliphorinae+Luciliinae is well supported, but the phylogenomic data cannot confidently place the remaining blowfly subfamilies (Helicoboscinae, Ameniinae, Chrysomyinae). Compared to hypotheses from the Sanger sequencing era, many clades within the muscoid grade are congruent but now have much higher support. Within much of Oestroidea, Sanger era and phylogenomic data struggle equally with regard to finding well-supported hypotheses.

First fossil of an oestroid fly (Diptera: Calyptratae: Oestroidea) and the dating of oestroid divergences.

Calyptrate flies include about 22,000 extant species currently classified into Hippoboscoidea (tsetse, louse, and bat flies), the muscoid grade (house flies and relatives) and the Oestroidea (blow flies, bot flies, flesh flies, and relatives). Calyptrates are abundant in nearly all terrestrial ecosystems, often playing key roles as decomposers, parasites, parasitoids, vectors of pathogens, and pollinators. For oestroids, the most diverse group within calyptrates, definitive fossils have been lacking. The first unambiguous fossil of Oestroidea is described based on a specimen discovered in amber from the Dominican Republic. The specimen was identified through digital dissection by CT scans, which provided morphological data for a cladistic analysis of its phylogenetic position among extant oestroids. The few known calyptrate fossils were used as calibration points for a molecular phylogeny (16S, 28S, CAD) to estimate the timing of major diversification events among the Oestroidea. Results indicate that: (a) the fossil belongs to the family Mesembrinellidae, and it is identified and described as Mesembrinella caenozoica sp. nov.; (b) the mesembrinellids form a sister clade to the Australian endemic Ulurumyia macalpinei (Ulurumyiidae) (McAlpine's fly), which in turn is sister to all remaining oestroids; (c) the most recent common ancestor of extant Calyptratae lived just before the K-Pg boundary (ca. 70 mya); and (d) the radiation of oestroids began in the Eocene (ca. 50 mya), with the origin of the family Mesembrinellidae dated at ca. 40 mya. These results provide new insight into the timing and rate of oestroid diversification and highlight the rapid radiation of some of the most diverse and ecologically important families of flies. ZooBank accession number-urn:lsid:zoobank.org:pub:0DC5170B-1D16-407A-889E-56EED3FE3627.