title: 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.
authors.affiliation: Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551.
authors.forename: Ana Carolina M
authors.initials: AC
authors.lastname: Junqueira
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética and Departamento de Genética, Evolução e Bioagentes, Universidade Estadual de Campinas, Campinas, SP, 13083-875, Brazil.
authors.forename: Ana Maria L
authors.initials: AM
authors.lastname: Azeredo-Espin
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética and Departamento de Genética, Evolução e Bioagentes, Universidade Estadual de Campinas, Campinas, SP, 13083-875, Brazil.
authors.forename: Daniel F
authors.initials: DF
authors.lastname: Paulo
authors.affiliation: Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Departamento de Biologia, Universidade de São Paulo, Ribeirão Preto, SP, 14040-901, Brazil.
authors.forename: Marco Antonio T
authors.initials: MA
authors.lastname: Marinho
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
authors.forename: Lynn P
authors.initials: LP
authors.lastname: Tomsho
authors.affiliation: Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551.
authors.forename: Daniela I
authors.initials: DI
authors.lastname: Drautz-Moses
authors.affiliation: Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551.
authors.forename: Rikky W
authors.initials: RW
authors.lastname: Purbojati
authors.affiliation: Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA.
authors.forename: Aakrosh
authors.initials: A
authors.lastname: Ratan
authors.affiliation: Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551.
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D044822:Biodiversity; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000302:isolation & purification; D004175:Diptera / Q000145:classification / Q000235:genetics*; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial