Abstract
True flies are insects of the order Diptera and encompass one of the most diverse groups of animals on Earth. Within dipterans, Schizophora represents a recent radiation of insects that was used as a model to develop a pipeline for generating complete mitogenomes using various sequencing platforms and strategies. 91 mitogenomes from 32 different species were sequenced and assembled with high fidelity, using amplicon, whole genome shotgun or single molecule sequencing approaches. Based on the novel mitogenomes, we estimate the origin of Schizophora within the Cretaceous-Paleogene (K-Pg) boundary, about 68.3 Ma. Detailed analyses of the blowfly family (Calliphoridae) place its origin at 22 Ma, concomitant with the radiation of grazing mammals. The emergence of ectoparasitism within calliphorids was dated 6.95 Ma for the screwworm fly and 2.3 Ma for the Australian sheep blowfly. Varying population histories were observed for the blowfly Chrysomya megacephala and the housefly Musca domestica samples in our dataset. Whereas blowflies (n = 50) appear to have undergone selective sweeps and/or severe bottlenecks in the New World, houseflies (n = 14) display variation among populations from different zoogeographical zones and low levels of gene flow. The reported high-throughput mitogenomics approach for insects enables new insights into schizophoran diversity and population history of flies.
Highlights
True flies are insects that undergo complete metamorphosis and belong to the two-winged insects order Diptera
Mitochondrial genomes were sequenced from whole insects, body parts and ethanol-preserved specimens using three different techniques: (i) a combination of long-range PCR and shotgun sequencing; (ii) whole genome shotgun (WGS) sequencing of genomic DNA using Illumina short reads; and (iii) WGS sequencing of genomic DNA using long reads from single molecule real time (SMRT) sequencing
For the 32 schizophoran species sequenced, 16 mtDNAs were assembled using a combination of long-range PCR and shotgun sequencing, and 16 were recovered using the WGS technique
Summary
True flies are insects that undergo complete metamorphosis and belong to the two-winged insects order Diptera. Studies targeting a wide range of insect diversity depend on more universally applicable methods One such approach is the whole genome shotgun (WGS) sequencing of total DNA. Mitochondrial genomes were sequenced from whole insects, body parts and ethanol-preserved specimens using three different techniques: (i) a combination of long-range PCR and shotgun sequencing; (ii) WGS sequencing of genomic DNA using Illumina short reads; and (iii) WGS sequencing of genomic DNA using long reads from single molecule real time (SMRT) sequencing. These strategies allowed us to increase the taxonomic breadth of dipteran phylogenies and calculate divergence dates for major Schizophora clades. Our results contribute to the comparative mitogenomics and population-based analyses of invertebrates and enable the generation of molecular data in an automated high-throughput fashion for insects in general
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