title: Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae).
abstract: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization.
  
  
  
  We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family.
  
  
  
  Anchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology.
authors.affiliation: Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada. adyoung@gmail.com.|Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada. adyoung@gmail.com.
authors.forename: Andrew Donovan
authors.initials: AD
authors.lastname: Young
authors.affiliation: Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32306-4102, USA.
authors.forename: Alan R
authors.initials: AR
authors.lastname: Lemmon
authors.affiliation: Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.|Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
authors.forename: Jeffrey H
authors.initials: JH
authors.lastname: Skevington
authors.affiliation: Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for Animal Biodiversity, Adenauerallee 160, Bonn, D-53113, Germany.
authors.forename: Ximo
authors.initials: X
authors.lastname: Mengual
authors.affiliation: Finnish Museum of Natural History, University of Helsinki, Zoology unit, P.O.Box 17, FIN-00014, Helsinki, Finland.
authors.forename: Gunilla
authors.initials: G
authors.lastname: Ståhls
authors.affiliation: Naturalis Biodiversity Center, EIS, P.O. Box 9517, 2300 RA, Leiden, The Netherlands.
authors.forename: Menno
authors.initials: M
authors.lastname: Reemer
authors.affiliation: Invertebrates Section, Royal Museum for Central Africa, Leuvensesteenweg 13, 3080, Tervuren, Belgium.
authors.forename: Kurt
authors.initials: K
authors.lastname: Jordaens
authors.affiliation: Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
authors.forename: Scott
authors.initials: S
authors.lastname: Kelso
authors.affiliation: Department of Biological Science, Florida State University, 319 Stadium Dr., P.O. Box 3064295, Tallahassee, FL, 32306-4295, USA.
authors.forename: Emily Moriarty
authors.initials: EM
authors.lastname: Lemmon
authors.affiliation: Plant Pest Diagnostics Branch, California Department of Food & Agriculture, 3294 Meadowview Road, Sacramento, CA, 95832-1448, USA.
authors.forename: Martin
authors.initials: M
authors.lastname: Hauser
authors.affiliation: Invertebrates Section, Royal Museum for Central Africa, Leuvensesteenweg 13, 3080, Tervuren, Belgium.
authors.forename: Marc
authors.initials: M
authors.lastname: De Meyer
authors.affiliation: Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für molekulare Biodiversitätsforschung, Adenauerallee 160, Bonn, D-53113, Germany.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Misof
authors.affiliation: Department of Entomology, North Carolina State University, Raleigh, NC, 27695, USA.
authors.forename: Brian M
authors.initials: BM
authors.lastname: Wiegmann
mesh_terms: D000818:Animals; D005075:Biological Evolution; D004175:Diptera / Q000145:classification* / Q000235:genetics; D035264:Flowers; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D054817:Pollination; D017422:Sequence Analysis, DNA
keywords: Anchored phylogenetics; Eristalinae; Flower flies; Hoverflies; Hybrid enrichment; Microdontinae; Pipizinae; Syrphinae