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A DNA Barcode Library for Germany0s Mayflies, Stoneflies and Caddisflies (Ephemeroptera, Plecoptera and Trichoptera)

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A DNA Barcode Library for Germany0s Mayflies, Stoneflies and Caddisflies (Ephemeroptera, Plecoptera and Trichoptera) Received: 12 December 2016 | Revised: 7 April 2017 | Accepted: 19 April 2017 DOI: 10.1111/1755-0998.12683 RESOURCE ARTICLE A DNA barcode library for Germany0s mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) Jer ome^ Moriniere 1 | Lars Hendrich1 | Michael Balke1,2 | Arne J. Beermann3 | Tobias Konig€ 1 | Monika Hess4 | Stefan Koch5 | Reinhard Muller€ 6 | Florian Leese3,7 | Paul D. N. Hebert8 | Axel Hausmann1,2 | Christoph D. Schubart9 | Gerhard Haszprunar1,2 1Bavarian State Collection of Zoology (SNSB - ZSM), Munchen,€ Germany Abstract 2Department Biology II and GeoBioCenter, Mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) are Ludwig-Maximilians-University, Munchen,€ prominent representatives of aquatic macroinvertebrates, commonly used as indica- Germany 3Aquatic Ecosystem Research, University of tor organisms for water quality and ecosystem assessments. However, unambiguous Duisburg-Essen, Essen, Germany morphological identification of EPT species, especially their immature life stages, is a 4 € € Buro H2 Okologische Gutachten, Hess & challenging, yet fundamental task. A comprehensive DNA barcode library based Heckes GbR, Munchen,€ Germany 5Independent Researcher, Mindelheim, upon taxonomically well-curated specimens is needed to overcome the problematic Germany identification. Once available, this library will support the implementation of fast, 6 Planungsburo€ Hydrobiologie, Berlin, cost-efficient and reliable DNA-based identifications and assessments of ecological Germany status. This study represents a major step towards a DNA barcode reference library 7Center for Water and Environmental Research (ZWU), University of Duisburg- as it covers for two-thirds of Germany’s EPT species including 2,613 individuals Essen, Essen, Germany belonging to 363 identified species. As such, it provides coverage for 38 of 44 fami- 8Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada lies (86%) and practically all major bioindicator species. DNA barcode compliant 9Zoology/Evolutionary Biology, University sequences (≥500 bp) were recovered from 98.74% of the analysed specimens. of Regensburg, Regensburg, Germany Whereas most species (325, i.e., 89.53%) were unambiguously assigned to a single Correspondence Barcode Index Number (BIN) by its COI sequence, 38 species (18 Ephemeroptera, ^ Jerome Moriniere, Bavarian State Collection nine Plecoptera and 11 Trichoptera) were assigned to a total of 89 BINs. Most of of Zoology (SNSB - ZSM), Munchen,€ Germany. these additional BINs formed nearest neighbour clusters, reflecting the discrimina- Email: [email protected] tion of geographical subclades of a currently recognized species. BIN sharing was Funding information uncommon, involving only two species pairs of Ephemeroptera. Interestingly, both German Federal Ministry of Education and maximum pairwise and nearest neighbour distances were substantially higher for Research; Bavarian State Ministry of Education and Culture, Science and the Arts Ephemeroptera compared to Plecoptera and Trichoptera, possibly indicating older speciation events, stronger positive selection or faster rate of molecular evolution. KEYWORDS barcode library, bioindicators, COI, cryptic diversity, DNA barcoding, Ephemeroptera, Germany, mitochondrial DNA, Plecoptera, Trichoptera, water quality 1 | INTRODUCTION (Baird & Sweeney, 2011; Hering et al., 2004; Illies & Schmitz, 1980; Kolkwitz & Marsson, 1909; Liebmann, 1951; Meier et al., 2006; Pan- Three aquatic insect orders, the mayflies (Ephemeroptera), stoneflies tle & Buck, 1955; Rolauffs, Hering, Sommerhauser,€ J€ahnig, & Rodi-€ (Plecoptera) and caddisflies (Trichoptera), also known as EPT, are ger, 2003; Sweeney, Battle, Jackson, & Dapkey, 2011; Zhou et al., often used as biological indicators in freshwater quality assessments 2011) and ecological studies (Bohmer,€ Rawer-Jost, & Zenker, 2003; | Mol Ecol Resour. 2017;17:1293–1307. wileyonlinelibrary.com/journal/men © 2017 John Wiley & Sons Ltd 1293 1294 | MORINIERE ET AL. Bohmer€ et al., 1999; Braukmann & Biss, 2004; Lorenz, Hering, Feld, Neu, 2013; Reusch & Weinzierl, 1999). The corresponding data are & Rolauffs, 2004; Schmedtje & Colling, 1996; Scholl,€ Haybach, & the result of the DNA barcoding projects overseen by the Bavarian Konig,€ 2005; Vannote, Minshall, Cummins, Sedell, & Cushing, 1980). State Collection of Zoology in Munich (SNSB-ZSM—www.barcoding. Bioindicator species are often used to survey the health of ecosys- zsm.de) through the “Barcoding Fauna Bavarica project” (BFB— tems, as they exhibit strong responses to pollution, mining, fracking www.faunabavarica.de—Haszprunar, 2009) launched in 2009, and by or climate change (Alvarez-Troncoso, Benetti, Sarr, Perez-Bilbao, & the “German Barcode of Life project” (GBOL—www.bolgermany.de) Garrido, 2015; Burton et al., 2014; Dedieu, Rhone, Vigouroux, & launched in 2012 (Geiger et al., 2015). Within the framework of the Cer eghino, 2015; Wallace, Grubaugh, & Whiles, 1996; Wiederholm, International Barcode of Life (iBOL) project, and in close cooperation 1984; Zhou et al., 2011). Therefore, an unambiguous identification with the Biodiversity Institute of Ontario (BIO, Guelph, Canada), the of EPT species is a crucial step for investigations of freshwater qual- German barcoding projects are assembling a DNA barcode library for ity, ecology and possible change or loss of biodiversity (Macher all animal species present in this country. Both projects together et al., 2016). have accumulated records for more than 20,000 animal species to Despite their importance for the assessment of freshwater the Barcode of Life Database (BOLD—www.boldsystems.org; Rat- ecosystems, accurate morphological delineation of most EPT species, nasingham & Hebert, 2007), with a special focus on the insect orders especially females and immatures, remains a challenging task, even Coleoptera (Hendrich et al., 2015), Heteroptera (Raupach et al., for experts, as some traits necessary for reliable identification are 2014), Hymenoptera (Schmidt, Schmid-Egger, Moriniere, Haszprunar, only present in one sex or at a certain stage of development (Zhou, & Hebert, 2015), Lepidoptera (Hausmann, Haszprunar, & Hebert, Adamowicz, Jacobus, DeWalt, & Hebert, 2009; Zhou et al., 2011). 2011a; Hausmann et al., 2011b), Neuroptera (Moriniere et al., 2014) Morphological identifications of these freshwater invertebrates are and Orthoptera (Hawlitschek et al., 2016). Aside from extending therefore not only extremely time-consuming and hence costly, but parameterization of the barcode reference library, work is now being often result in misidentifications, making any assessments of impact directed towards developing the methods and techniques, such as highly problematic (Haase, Pauls, Schindehutte,€ & Sundermann, high-throughput DNA metabarcoding (Moriniere et al., 2016), to 2010; Haase et al., 2006; Pfrender et al., 2010). Moreover, despite allow large-scale identification of bioindicator species within bulk the growing need for taxonomic expertise to support ecosystem samples of benthic organisms. assessments, the number of well-trained taxonomists is decreasing (New, 1996; Stribling, Moulton, & Lester, 2003; Wheeler, 2014). In 2 | MATERIALS AND METHODS this context, DNA barcoding provides an effective way to overcome the difficulties in morphological identifications, as this technology 2.1 | Fieldwork delivers fast, efficient and reliable species identification (Hausmann, Parisi, & Sciarretta, 2015; Hausmann et al., 2016; Hebert, Cywinska, A network of researchers and professional taxonomists, mainly work- Ball, & DeWaard, 2003b; Hebert, Ratnasingham, & de Waard, ing as consultants for water quality assessment studies, and a num- 2003a; Miller, Hausmann, Hallwachs, & Janzen, 2016; Vane-Wright, ber of citizen scientists collected specimens of EPTs from Smith, & Kitching, 1994), even in areas where only little information throughout Germany, with a focus on southern Germany. Field work on the benthic macroinvertebrate fauna is present (Geraci, Al-Saffar, permits were issued by the responsible state environmental offices & Zhou, 2011; Ibrahimi, Kucinic, Gashi, & Kotori, 2012). A well- in Bavaria [Bayerisches Staatsministerium fur€ Umwelt und Gesund- curated, comprehensive DNA barcode library based upon voucher heit, for the project: “Barcoding Fauna Bavarica”]. The study sites species is the foundation for such applications (Ball, Hebert, Burian, included more than 573 localities in state forests, peatlands, lakes & Webb, 2005; Boumans & Brittain, 2012; Gattolliat, Cavallo, Vua- and rivers, and also protected areas such as the national parks “Bay- taz, & Sartori, 2015; Kjaerstad, Webb, & Ekrem, 2012; Ruiter, Boyle, erischer Wald” and “Berchtesgadener Land” (Appendix S1). & Zhou, 2013; Salokannel, Rantala, & Wahlberg, 2010; Vuataz, Sar- tori, Wagner, & Monaghan, 2011; Webb et al., 2012; Zhou et al., 2.2 | Specimen sampling 2009, 2011, 2016), as it also enables promising future applications such as environmental DNA barcoding (Baird & Hajibabaei, 2012; Most voucher specimens were collected from Germany (2,564), but Carew, Pettigrove, Metzeling, & Hoffmann, 2013; Hajibabaei, Shok- a few specimens were derived from nearby nations including Austria ralla, Zhou, Singer, & Baird, 2011; Hajibabaei, Spall, Shokralla, & van (18), Croatia (1), France (28) and northern Italy (2). Specimens are Konynenburg, 2012; Shokralla, Spall, & Gibson, 2012) and metabar- deposited in SNSB-ZSM, Zoologisches
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