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Comparative Genetic Analysis of Grayling (Thymallus Sp.) from Central Asia (Kazakhstan, Russia and Mongolia)

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Comparative Genetic Analysis of Grayling (Thymallus Sp.) from Central Asia (Kazakhstan, Russia and Mongolia) Comparative genetic analysis of grayling (Thymallus sp.) from Central Asia (Kazakhstan, Russia and Mongolia) Master’s Thesis In Partial Fulfillment of the Requirements for the Degree Master of Science at the Karl-Franzens University of Graz Jacqueline Grimm Institute of Zoology Supervisor: Assoc. Prof. Dr. Steven Weiss September 2015 TABLE OF CONTENTS ABSTRACT .............................................................................................................................. iii ZUSAMMENFASSUNG .......................................................................................................... iv ACKNOWLEDGEMENT ......................................................................................................... v 1 INTRODUCTION ................................................................................................................... 1 1.1 Phylogeography and its importance ................................................................................. 1 1.2 Perspectives of Siberian paleo-history ............................................................................. 1 1.3 Importance of Salmonidae and the genus Thymallus ....................................................... 2 1.4 Thymallus species in Eurasia ............................................................................................ 3 1.5 The central Asian basin and its Thymallus inhabitants..................................................... 5 1.6 Research questions ........................................................................................................... 6 2 MATERIAL & METHODS .................................................................................................... 7 2.1 Sampling and DNA extraction ......................................................................................... 7 2.2 Genetic analyses - mtDNA ............................................................................................... 7 2.2.1 Amplification and sequencing ................................................................................... 7 2.2.2 Sequence alignment and phylogenetic analyses ........................................................ 8 2.2.3 Haplotype network analysis ..................................................................................... 12 2.3 Genetic analyses – microsatellites (SSR) ....................................................................... 12 2.3.1 Amplification and screening .................................................................................... 12 2.3.2 Basic population genetic statistics ........................................................................... 14 2.4 Genetic analysis – mixed data set ................................................................................... 15 3 RESULTS .............................................................................................................................. 16 3.1 Inhabitants of the Khovd River basin ............................................................................. 16 3.1.1 Genetic diversity of Thymallus sp., classified in studied water bodies ................... 16 3.1.2 Population structure of Thymallus sp., classified in studied water bodies............... 17 3.1.3 Genetic diversity of samples, classified in different taxa of Thymallus .................. 19 3.1.4 Population structure of samples, classified in different taxa of Thymallus ............. 19 3.2 Lineage relationship of Thymallus sp. from Kazakhstan ............................................... 21 3.2.1 Microsatellite analysis of genetic diversity.............................................................. 21 3.2.2 Microsatellite analysis of population structure ........................................................ 22 3.2.3 Phylogenetic relationships using mtDNA ................................................................ 25 3.2.4 Divergence times and population history using mixed data set ............................... 29 i 4 DISCUSSION ....................................................................................................................... 32 4.1 General genetic differentiation ....................................................................................... 32 4.2 Thymallus inhabiting the Khovd river basin ................................................................... 33 4.3 Taxonomic assignment of populations from Kazakhstan ............................................... 34 REFERENCES ......................................................................................................................... 35 LIST OF FIGURES .................................................................................................................. 42 APPENDIX .............................................................................................................................. 44 ii ABSTRACT Siberia is a vast region containing four of the world’s ten largest freshwater rivers. The region’s fish diversity was affected by large-scale hydrological dynamics during the glacial and postglacial periods. The wide-spread populations of the genus Thymallus arouse interest of phylogeographers, aiming to improve knowledge on the history of these paleo-hydrological events. The first phylogeographic analysis supported that distinct mitochondrial (mtDNA) lineages belong to major drainage systems. Recent molecular research, coupled with systematic morphological analysis exposed the within-basin diversity and extreme population substructure of graylings. Despite numerous studies, the number of species and their systematic scheme are still unclear. In this study, seven microsatellite loci were used to increase the genetic resolution of previously published data on grayling of the Khovd River basin in Mongolia. The central question focused on whether or not the basin’s phenotypic diversity comprised one (i.e. T. brevirostris) or more species. Additionally, data on the mtDNA control region and flanking transfer RNA genes were combined with microsatellite data to assess the population genetic structure and lineage relationship of Thymallus from the upper reaches of the Irtysh River, in Kazakhstan, including Lake Markakol. Allelic variation of microsatellites revealed no evidence of multiple species in the Central Asian basin and suggests that phenotypic variation in Mongolian grayling is the result of rapid adaptation to different habitats. Results of both mtDNA and microsatellite analysis support a sister relationship between Mongolian grayling (T. brevirostris) and grayling of the upper reaches of the Irtysh (T. sp.). These grayling, together with four other described taxa of the region (T. nikolskyi, T. svetovidovi, T. nigrescens, T. baicalensis), spread across three major river basins, are relatively closely related and presumed to have a common ancestor. iii ZUSAMMENFASSUNG Sibirien ist ein riesiges Gebiet, das vier der zehn größten Süßwasserflüsse besitzt. Die Vielfalt der Fische dieses Gebietes wurde während glazialer und postglazialer Perioden von großräumig hydrologischen Bewegungen beeinflusst. Die weit verbreiteten Populationen von Thymallus erweckten das Interesse der Phylogeographen, die das Wissen über den Verlauf dieser paleohydrologischen Ereignisse erweitern wollten. Laut erster phylogeographischer Analysen gehörten spezifische mitochondriale Linien zu Hauptwassersystemen. Systematische Morphologieanalysen und jüngste molekulare Forschungen deckten die Diversität der Äsche innerhalb eines Beckens und ihre ausgeprägte Populationsstruktur auf. Die Zahl der Arten und ihre Systematik ist jedoch noch unklar. In dieser Studie wurden sieben Mikrosatelliten verwendet, um die genetische Auflösung zuvor publizierter Daten von Äschen aus dem Einzugsgebiet des Khovds in der Mongolei zu verbessern. Es stellte sich die Frage, ob sich die Diversität des Phänotyps im Becken aus einer (T. brevirostris) oder mehrerer Arten zusammensetzt. Mittels mtDNA Kontroll-Region, angrenzender Transfer-RNA-Gene und Mikrosatelitten wurde die populationsgenetische Struktur und Abstammungsbeziehung von Thymallus aus dem Oberlauf des Irtyshs in Kasachstan, sowie des Sees Markakol, erhoben. Die Allelvariabilität der Mikrosatelliten gab keinen Hinweise auf mehrere Arten im zentralasiatischen Becken und schließt daraus, dass phänotypische Unterschiede der mongolischen Äsche die Folge einer raschen Anpassung an unterschiedliche Lebensräume ist. Analysen der mtDNA und Mikrosatelliten weisen auf ein Schwesternverhältnis zwischen mongolischer Äsche (T. brevirostris) und der Äsche aus Kasachstan (T. sp.) hin. Zusammen mit vier weiteren Taxa dieser Region (T. nikolskyi, T. svetovidovi, T. nigrescens, T. baicalensis) sind sie über drei Hauptwassersysteme verteilt, relativ nahe miteinander verwandt und es wird angenommen, dass sie einen gemeinsamen Vorfahren besitzen. iv ACKNOWLEDGEMENT I would like to take the opportunity to thank the people who spent their time and shared their knowledge for helping me to complete my thesis with the best possible result. First, I would like to give my special thanks to my supervisor, Assoc. Prof. Dr. Steven Weiss, for the patient guidance, encouragement and advice he has provided throughout my time as his student. I am very grateful to have a supervisor who cared so much about my work, and who responded to my questions and queries so promptly. I want to thank Dr. Igor Knizhin from the Irkutsk State University (ISU), for providing some samples, creating the very comprehensive
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