Monophyletic blowflies revealed by phylogenomics

Abstract

Background: Blowflies are ubiquitous insects, often shiny and metallic, and the larvae of many species provide important ecosystem services (e.g., recycling carrion) and are used in forensics and debridement therapy. Yet, the taxon has repeatedly been recovered to be para- or polyphyletic, and the lack of a well-corroborated phylogeny has prevented a robust classification.

Results: We here resolve the relationships between the different blowfly subclades by including all recognized subfamilies in a phylogenomic analysis using 2221 single-copy nuclear protein-coding genes of Diptera. Maximum likelihood (ML), maximum parsimony (MP), and coalescent-based phylogeny reconstructions all support the same relationships for the full data set. Based on this backbone phylogeny, blowflies are redefined as the most inclusive monophylum within the superfamily Oestroidea not containing Mesembrinellidae, Mystacinobiidae, Oestridae, Polleniidae, Sarcophagidae, Tachinidae, and Ulurumyiidae. The constituent subfamilies are re-classified as Ameniinae (including the Helicoboscinae, syn. nov.), Bengaliinae, Calliphorinae (including Aphyssurinae, syn. nov., Melanomyinae, syn. nov., and Toxotarsinae, syn. nov.), Chrysomyinae, Luciliinae, Phumosiinae, Rhiniinae stat. rev., and Rhinophorinae stat. rev. Metallic coloration in the adult is shown to be widespread but does not emerge as the most likely ground plan feature.

Conclusions: Our study provides the first phylogeny of oestroid calyptrates including all blowfly subfamilies. This allows settling a long-lasting controversy in Diptera by redefining blowflies as a well-supported monophylum, and blowfly classification is adjusted accordingly. The archetypical blowfly trait of carrion-feeding maggots most likely evolved twice, and the metallic color may not belong to the blowfly ground plan.

Keywords: Calyptratae; Coloration; Genome; Phylogeny; Transcriptome.

Fig. 1

Representative taxa of calliphorids, Mesembrinellidae and Polleniidae. A, B Calliphorinae. A Calliphora sp. B Calliphora sp., larvae feeding on dead bird. C, D Chrysomyinae. C Chrysomya sp. D Chrysomya albiceps, larvae feeding on dead hedgehog. E, F Luciliinae. E Lucilia sp. F Lucilia sp., larvae feeding on dead bird. G Ameniinae (Amenia sp.). H Bengaliinae (Bengalia sp.). I Helicoboscinae (Eurychaeta palpalis). J Melanomyinae (Melinda viridicyanea). K, L Phumosiinae. K Caiusa sp. L – Caiusa sp., egg on foam mass of the shrub frog Chiromantis nongkhorensis [5] (reproduced with permission from copyright holder). M Polleniidae (Pollenia sp.). N Mesembrinellidae (Mesembrinella sp.). O Rhiniidae (Stomorhina lunata). P Rhinophoridae (Rhinophora lepida). A, B, G, H, I, J, O, and P are from Flickr; C, D, E, F, and M are from Diptera.info; K is from antroom

Fig. 2

Phylogeny of Oestroidea in previous studies. A McAlpine [11] (morphology). B Rognes [12] (morphology). C Kutty et al. [13] (combination of mitochondrial and nuclear genes). D Marinho et al. [14] (combination of mitochondrial and nuclear genes). E Singh & Wells [15] (combination of mitochondrial and nuclear genes). F Zhang et al. [16] (mitogenomic data). G Cerretti et al. [17] (combination of mitochondrial and nuclear genes). H Marinho et al. [18] (combination of mitochondrial and nuclear genes). I Kutty et al. [19] (phylotranscriptomic data). J Buenaventura et al. [20] (ultra-conserved elements)

Fig. 3

Maximum likelihood (ML) tree inferred from the amino acid matrix of dataset Dref_Ltax, with support values of ML bootstrap (MLBS), maximum parsimony jackknife (MPJK), and ASTRAL bootstrap (Astral BS) presented at nodes. The flies on the branches indicate origins of adult metallic color within calliphorids. The asterisk (*) and hyphen (-) at nodes indicate full support and branch not recovered, respectively. Species marked with asterisk (*) are sequenced with genomic data. Ingroup branches are colored according to family classification, as explained in the legend

Fig. 4

Phylogenetic topology compared between reconstructions based on datasets with larger (left) and smaller (right) taxon sampling. Numbers above nodes of the left cladogram are maximum likelihood (ML) bootstrap values of phylogeny inferred from the dataset Dref_Ltax of amino acid (AA), 2nd-codon positions (NT2), 1st & 2nd-codon position (NT12), and maximum parsimony jackknife value of phylogeny inferred from the dataset of amino acid (AA). Numbers below nodes of the left cladogram are ML bootstrap values of phylogeny inferred from dataset of AA, NT2, NT12, and MP jackknife value of phylogeny inferred from AA of dataset Aref_Ltax. Numbers above nodes of the right cladogram are ML bootstrap values of phylogeny inferred from dataset of AA, NT2, NT12, and MP jackknife value of phylogeny inferred from AA of dataset Dref_Stax. Numbers below nodes of the right cladogram are ML bootstrap values of phylogeny inferred from dataset of AA, NT2, NT12, and MP jackknife value of phylogeny inferred from AA of dataset Aref_Stax. The reddish boxes indicate nodes which conflict between analyses

Fig. 5

Results of partition log-likelihood analyses in terms of phylogenetic position of Chrysomyinae using amino acid alignments of dataset Dref_Ltax. A The three topologies. B, C Ranked distribution of ΔpLi of 2221 genes under the model estimated by IQ-TREE. B Genes favoring T1 (positive values) or T2 (negative values). C Genes favoring T1 (positive values) or T3 (negative values)

Fig. 6

Four-cluster likelihood mapping (FcLM) of the phylogenetic position of Chrysomyinae using amino acid alignments of dataset Dref_Ltax. A Group definitions. B, C Two variations of FcLM based on concatenated amino acid alignments shown as 2D graphs, with phylogeny modified by excluding group 2b (B) or by excluding group 2a (C)