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      Origin and diversification of hoverflies: a revision of the genera Asarkina and Allobaccha – A BIG4 Consortium PhD project

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      Journal: Research Ideas and Outcomes
      Publisher: Pensoft Publishers

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          Abstract

          This BIG4 PhD project involves the overall taxonomic revision of the genera Allobaccha Curran and Asarkina Macquart (Diptera: Syrphidae). The revisions will be divided by biogeographic region (Afrotropical and Indomalayan) and published accordingly. The publications will be collated as a thesis for submission to the University of Bonn (Rheinische Friedrich-Wilhelms-Universität Bonn, Germany) doctoral program of biology. The goal of this project is to resolve alpha taxonomy and to infer the phylogenetic placement of these genera within the Syrphidae using Next-Generation Sequencing and Anchored Hybrid Enrichment techniques. The techniques undertaken in this project will be applied to future systematic problems in Diptera and testing future phylogenetic hypotheses.

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          Syrphidae: can they be used as environmental bioindicators?

          Daniele Sommaggio (1999)
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            Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae)

            Andrew Young, Alan Lemmon, Jeffrey H. Skevington … (2016)
            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.
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              BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design.

              Christoph Mayer, Manuela Sann, Alexander Donath … (2016)
              Target DNA enrichment combined with high-throughput sequencing technologies is a powerful approach to probing a large number of loci in genomes of interest. However, software algorithms that explicitly consider nucleotide sequence information of target loci in multiple reference species for optimizing design of target enrichment baits to be applicable across a wide range of species have not been developed. Here we present an algorithm that infers target DNA enrichment baits from multiple nucleotide sequence alignments. By applying clustering methods and the combinatorial 1-center sequence optimization to bait design, we are able to minimize the total number of baits required to efficiently probe target loci in multiple species. Consequently, more loci can be probed across species with a given number of baits. Using transcript sequences of 24 apoid wasps (Hymenoptera: Crabronidae, Sphecidae) from the 1KITE project and the gene models of Nasonia vitripennis, we inferred 57,650, 120-bp-long baits for capturing 378 coding sequence sections of 282 genes in apoid wasps. Illumina reduced-representation library sequencing confirmed successful enrichment of the target DNA when applying these baits to DNA of various apoid wasps. The designed baits furthermore enriched a major fraction of the target DNA in distantly related Hymenoptera, such as Formicidae and Chalcidoidea, highlighting the baits' broad taxonomic applicability. The availability of baits with broad taxonomic applicability is of major interest in numerous disciplines, ranging from phylogenetics to biodiversity monitoring. We implemented our new approach in a software package, called BaitFisher, which is open source and freely available at https://github.com/cmayer/BaitFisher-package.git.
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                Author and article information

                Journal
                Title: Research Ideas and Outcomes
                Abbreviated Title: RIO
                Publisher: Pensoft Publishers
                ISSN (Electronic): 2367-7163
                Publication date Created: August 07 2017
                Publication date (Electronic): August 07 2017
                Volume: 3
                Page: e19860
                Article
                DOI: 10.3897/rio.3.e19860
                SO-VID: 8b4b9b99-e4da-47f7-a6a7-981063fb3f23
                Copyright © © 2017
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                http://creativecommons.org/licenses/by/4.0/

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