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DNA Barcoding of Austria's Biodiversity

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DNA Barcoding of Austria's Biodiversity DNA Barcoding of Austria’s Biodiversity KUMULATIVE DISSERTATION Zur Erlangung des akademischen Grades Dr. rer. nat. An der naturwissenschaftlichen Fakultät der Karl-Franzens-Universität Graz Institut für Biologie Eingereicht von Lukas Zangl, MSc Unter der Betreuung von Priv.Doz. Mag. Dr. Stephan Koblmüller Jänner 2021 Acknowledgments I would like to thank my many colleagues at the University of Graz and at the Natural History Museum Vienna for their cooperation in the course of my own research and for letting me partake in a range of diverse projects over the last few years. Particularly, among others, Max, Andrea, Sylvia, Gernot, Christoph, Philipp, Anna, Gernot, Wolfi, Tamara, Holger, Angi, Jacky, Marcia, Iris, Oliver, Frank, Lisi and Nikolaus provided me with ideas, help and inspiring discussions. I am also thankful to my mentor Kristina Sefc for her support and encouragement. Furthermore, I am grateful to my loving family and dear friends, among them Lukas, Martin, Rüdiger, Daniel, Bertram and Tina for their great support. Finally, I want to especially thank my supervisor Stephan Koblmüller for his continuous encouragement, support, supervision, inspiration, faith, his untiring motivation to look into something new every other day (and dragging me into it as well) and for being able to rely on him throughout the entire time of my PhD. 2 Table of contents Abstract ............................................................................................................................. 4 Zusammenfassung ............................................................................................................ 5 Introduction ...................................................................................................................... 7 Main part ........................................................................................................................ 12 Chapter 1 ..................................................................................................................... 12 Chapter 2 ..................................................................................................................... 35 Chapter 3 ..................................................................................................................... 48 Chapter 4 ..................................................................................................................... 78 Chapter 5 ................................................................................................................... 109 Chapter 6 ................................................................................................................... 122 Chapter 7 ................................................................................................................... 134 Discussion ..................................................................................................................... 152 References .................................................................................................................... 156 3 Abstract DNA barcoding has evolved to one of the prime tools in biodiversity research over the past two decades. This method utilizes reliable reference databases for the comparison of standard marker sequences of unknown samples of specimens in order to facilitate species assignment. Consequently, it can be used for the determination and discrimination of species, for the detection of alien/invasive species or species new to science, to uncover cryptic diversity and pinpoint cases for systematic and/or taxonomic inquiry and for any applied approach in need to determine a biological species. Contrasting to these strengths, it shows some well-known and extensively debated weaknesses like barcode sharing or insufficient resolution in cases of recent divergence, introgressive events or hybridization, issues with wet lab protocols, a need for a certain infrastructure and the competition with the rapidly expanding field of genomics. However, the “Austrian Barcode of Life” initiative (ABOL) aligns to a plethora of other national and international barcoding projects using this very technique in order to create comprehensive national reference species inventories. The quality and completeness of those databases -also a recurrent topic of discussion- poses the basis for all applied approaches as well as methodological alterations of the classical DNA barcoding like the use of mini-barcodes, high-resolution melting analyses (HRM) or non-invasive and community-level assessments via environmental DNA sequencing (eDNA). In the course of my PhD in the framework of ABOL, I used DNA barcoding to i) generate a comprehensive national species inventory for the Austrian amphibians and reptiles, ii) investigate the genetic diversity of a specific fish family in the Austrian Danube system, iii) confirm the description of a fish species new to science and the presence of alien/invasive vertebrate and invertebrate species in Austria, iv) set up a high-resolution melting analysis workflow for the discrimination of closely related beetle species which can be adapted for similar applications and v) to uncover potential cryptic diversity in snow scorpionflies which points to the need of further morphological and genomic investigation to clarify systematic and taxonomic relationships. In summary, I used DNA barcoding for a wide range of applications, harnessing its strengths but also exploring and reaching its limitations. Furthermore, I showed how these weaknesses can be dealt with and what ways there are to supplement classical DNA barcoding in ambiguous cases. 4 Zusammenfassung In den vergangenen zwei Jahrzehnten entwickelte sich DNA-Barcoding zu einer der wichtigsten Methoden der Biodiversitätsforschung. Dieses Verfahren basiert auf dem Vergleich der Sequenzen standardisierter genetischer Marker von unbekannten Proben mit Referenzdatenbanken zur Artbestimmung. Somit kann es zur Bestimmung und Unterscheidung von Arten, zum Nachweis gebietsfremder/invasiver Arten oder der Entdeckung bisher unbeschriebener Arten, zum Aufzeigen kryptischer Diversität und von systematisch und/oder taxonomisch interessanten Fragestellungen und für angewandte Bereiche, in denen die Identität einer Probe von Bedeutung ist, verwendet werden. Diesen vermeintlichen Stärken stehen jedoch auch einige wohl bekannte und vielfältig diskutierte Schwächen gegenüber. Darunter finden sich unter anderem Fälle identer DNA-Barcodes, die gleichzeitig unterschiedliche Arten ausweisen („barcode sharing“), ungenügende Unterschiede in den DNA-Sequenzen entwicklungsgeschichtlich junger Arten oder in Fällen von Introgression oder Hybridisierung, Probleme bei der Bearbeitung im Larbor, die Notwendigkeit einer gewissen Infrastruktur oder die zunehmende Konkurrenz durch das stetig wachsende Gebiet der Genomik. Nichtsdestotrotz verwendet die „Austrian Barcode of Life“ Initiative (ABOL), ebenso wie viele andere nationale und internationale Barcoding-Projekte diese Methode zur Erstellung möglichst vollständiger taxonomischer Referenzdatenbanken. Die Qualität und Vollständigkeit dieser Datenbanken -ebenso ein viel diskutiertes Thema- stellt die Grundlage für alle Anwendungen sowie für alternative methodische Zugänge zum konventionellen DNA-Barcoding wie Mini-Barcodes, hochauflösende Schmelzverfahren (HRM) oder nicht-invasive und populationsbezogene Analysen mittels der Sequenzierung von Umwelt-DNA (eDNA) dar. Im Zuge meiner Dissertation im Rahmen von ABOL verwendete ich DNA-Barcoding um i) eine vollständige Referenzdatenbank der österreichischen Amphibien und Reptilien zu erstellen, ii) die genetische Diversität einer bestimmten Fischfamilie im österreichischen Donausystem zu untersuchen, iii) die Artbeschreibung einer bisher unbeschriebenen Fischart sowie die Nachweise gebietsfremder/invasiver Wirbeltiere und wirbelloser Tiere in Österreich zu bestätigen, iv) ein Verfahren basierend auf der Analyse hochauflösender Schmelzkurven zur Unterscheidung nah verwandter Käferarten zu etablieren, das auch für ähnliche Anwendungen adaptiert werden kann und v) um potentielle kryptische Diversität innerhalb der Winterhaften (Insecta: Mecoptera) nachzuweisen, was der 5 Untersuchung weiterer morphologischer sowie genomischer Daten bedurfte, um systematische und taxonomische Zusammenhänge aufzulösen. Somit habe ich DNA- Barcoding für eine Vielzahl unterschiedlicher Anwendungen verwendet und mir dessen Stärken zunutze gemacht, bin aber auch auf die inherenten Schwächen sowie die Limitierungen dieser Methode gestoßen. Darüberhinaus konnte ich Möglichkeiten aufzeigen, wie mit diesen Schwächen umgegangen und das klassische DNA-Barcoding in uneindeutigen Fällen mittels zusätzlicher Daten und Analysemethoden unterstützt werden kann. 6 Introduction The term ‘biological diversity’ or ‘biodiversity’ “… includes diversity within species, between species and of ecosystems …” according to the definition of the Convention on Biological Diversity ((CBD), United Nations 1993). In other words, it encompasses species richness (number of species), genetic diversity and the diversity of ecosystems. Austria, despite its small size compared to other European countries, houses a substantial wealth of this diversity due to its geographic location and topological and climatic features. It encompasses glacial mountain tops in the inner Alpine regions in Western and Central Austria, wooded areas at the foothills surrounding the Alps and parts of the Pannonian plains at the Eastern borders. This diversity
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