Large-scale mitogenomics enables insights into Schizophora (Diptera) radiation and population diversity

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.

Mitochondrial genomes of the hoverflies Episyrphus balteatus and Eupeodes corollae (Diptera: Syrphidae), with a phylogenetic analysis of Muscomorpha

“…Syrphidae (accession KM244713)91628. Here, we sequenced the mitochondrial genomes from Episyrphus and Eupeodes , representing the first mitochondrial genomes reported from the genera Episyrphus and Eupeodes .…”

Comparison of morphological, DNA barcoding, and metabarcoding characterizations of freshwater nematode communities

“…An integrated approach to species identification based on morphological and molecular analyses will yield a dataset with even greater reliability than based on only one method. Additionally, future methods, such as whole-genome sequencing and other PCR-free approaches (Junqueira et al, 2016;Orgiazzi, Dunbar, Panagos, Groot, & Lemanceau, 2015), will eliminate or at least minimize many of the current drawbacks of current molecular approaches, by obviating the need for primers. However, these methods require a high sequencing depth and a much larger number of whole genomes for nematodes in existing databases (Pompanon & Samadi, 2015).…”

“…With the decline in taxonomic expertise, newly developed molecular methods are being increasingly used in species identification, especially of organisms at the microscopic and microbial scales (Creer et al, 2016). Other applications of molecular methods include whole-genome analyses, the determination of evolutionary patterns in phylogeographic and phylogenetic studies (Blaxter et al, 2005;Derycke et al, 2008;Holterman et al, 2006;Junqueira et al, 2016), and initiatives aimed at collecting the planet's biodiversity in molecular databases. The latter relies on species identification using a single short gene fragment, the so-called barcoding approach (Hebert et al, 2003;Stoeckle & Stoeckle, 2003).…”

Sequencing and analyzing complete mitochondrial DNA ofMuscina angustifrons(Insecta, Diptera, Muscidae)

“…Therefore, correct identification of the insect species from crime scenes is crucial for forensic investigations. There are only two mitochondrial genome records from Muscina species in the GenBank which are M. stabulans (KM676394) from China and M. levida (KT272866) from U.S.A (Lan et al 2015;Junqueira et al 2016). In this study we are providing the complete mitochondrial genome of Muscina angustifrons.…”

“…The mitochondrial genome of M. angustifrons (GenBank Accession number: KY495724) has typical gene order and gene orientation with ancestral insect genome (Cameron 2014). It consist of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and one putative control region likewise the other Muscina records (Lan et al 2015;Junqueira et al 2016). …”