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Publication . Article . 2016

Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae)

Andrew D. Young; Alan R. Lemmon; Jeffrey H. Skevington; Ximo Mengual; Gunilla Ståhls; Menno Reemer; Kurt Jordaens; +6 Authors
Open Access
English
Published: 29 Jun 2016 Journal: BMC Evolutionary Biology, volume 16, issue 1 (issn: 1471-2148, Copyright policy )
Publisher: Springer Nature
Country: Finland
Abstract
Background 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. Results 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. Conclusions 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. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0714-0) contains supplementary material, which is available to authorized users.
Subjects by Vocabulary

Microsoft Academic Graph classification: Phylogenetic tree Monophyly Phylogenetics Eristalinae biology.organism_classification biology Microdontinae Taxon Paraphyly Systematics Evolutionary biology Zoology

Subjects

Ecology, Evolution, Behavior and Systematics, Flower flies ; Hybrid enrichment ; Syrphinae ; Anchored phylogenetics ; Microdontinae ; Hoverflies ; Eristalinae ; Pipizinae, Research Article, Anchored phylogenetics, Hybrid enrichment, Syrphinae, Microdontinae, Eristalinae, Pipizinae, Flower flies, Hoverflies, OBLIGATE PREDATOR, CHEMICAL MIMICRY, POLLINATION, SYSTEMATICS, EVOLUTION, BIOLOGY, HISTORY, LARVAL, CLASSIFICATION, 1181 Ecology, evolutionary biology

Funded by
NSF| Beyond Drosophila: Comparative transcriptomics of schizophoran flies to resolve a rapid radiation
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1257960
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
,
NSF| I-Corps: Anchored Hybrid Enrichment
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1313554
  • Funding stream: Directorate for Engineering | Division of Industrial Innovation & Partnerships
,
NSERC
Project
  • Funder: Natural Sciences and Engineering Research Council of Canada (NSERC)
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