ALBERT

Note: Dissertation, Universität Potsdam, 2017 , Content List of Abbreviations List of Figures List of Tables Summary Zusammenfassung Motivation Chapter 1 1. Scientific background 1.1 Late Quaternary climate changes and treeline transition in northern Siberia 1.2 Natural archives and proxies to assess vegetation history 1.3 Study area 1.3 Objectives of the thesis 1.4 Thesis outline 1.4.1 Chapters and manuscripts 1.4.2 Author's contribution 1.4.2.1 Manuscript I - published 1.4.2.2 Manuscript II - submitted 1.4.2.3 Manuscript III - prepared for submission Chapter 2 2. Manuscript I: Sedimentary ancient DNA and pollen reveal the composition of plant organic matter in Late Quaternary permafrost sediments of the Buor Khaya Peninsula (north-eastern Siberia) 2.1 Abstract 2.2 Introduction 2.3 Geographical settings 2.4 Material and methods 2.4.1 Core material 2.4.2 Subsampling of the permafrost core 2.4.3 Molecular genetic laboratory work 2.4.4 Analysis of sequence data and taxonomic assignments 2.4.5 Pollen sample treatment and analysis 2.4.6 Statistical analyses and visualization 2.5 Results 2.5.1 SedaDNA 2.5.1.1 SedaDNA of terrestrial plants 2.5.1.2 SedaDNA of swamp and aquatic plants 2.5.1.3 SedaDNA of bryophytes and algae 2.5.2 Pollen 2.5.2.1 Pollen of terrestrial plants 2.5.2.2 Pollen and spores of swamp and aquatic plants 2.5.2.3 Spores and algae 2.5.3 Ratios of terrestrial to swamp and aquatic taxa and Poaceae to Cyperaceae 2.6 Discussion 2.6.1 Quality and proxy value of sedaDNA and pollen data 2.6.2 Environmental conditions during the pre-LGM (54-51 kyr BP, 18.9-8.35 m) and composition of deposited organic matter 2.6.3 Environmental conditions during the post-LGM (11.4-9.7 kyr BP (13.4-11.1 cal kyr BP)) and composition of deposited organic matter 2.7 Conclusions 2.8 Acknowledgements Chapter 3 3. Manuscript II: Genetic variation of larches at the Siberian tundra-taiga ecotone inferred from the assembly of chloroplast genomes and mitochondrial sequences 3.1. Abstract 3.2. Introduction 3.3. Material and methods 3.3.1 Plant material 3.3.2 DNA isolation and sequencing 3.3.3 Sequence processing and de novo assembly 3.3.4 Chloroplast genome assembly, annotation and variant detection 3.3.5 Mitochondrial sequences 3.3.6 Analyses of genetic variation 3.4 Results 3.4.1 Chloroplast genome structure and genetic variation 3.4.2 Mitochondrial sequences and genetic variation 3.5 Discussion 3.5.1 De novo assembly and genetic variation of chloroplast genomes and mitochondrial sequences 3.5.2 The distribution of genetic variation at the tundra-taiga ecotone 3.6 Conclusions 3.7 Acknowledgements Chapter 4 4. Manuscript III: The history of tree and shrub taxa and past genetic variation of larches on Bol'shoy Lyakhovsky Island (New Siberian Archipelago) since the last interglacial uncovered by sedimentary ancient DNA 4.1 Abstract 4.2 Introduction 4.3 Materials and methods 4.3.1 Geographic setting 4.3.2 Core material 4.3.2.1 Core L14-02: Yedoma Ice Complex 4.3.2.2 Core L14-03: Thermo terrace 4.3.2.3 Core L14-04 and hand-pieces L14-04B and L14-04C: Thermo terrace including Eemian deposits 4.3.2.4 Core L14-05: Alas 4.3.3 Core sub-sampling 4.3.4 Molecular genetic laboratory work 4.3.4.1 Sedimentary ancient DNA metabarcoding approach 4.3.4.2 Specific amplification of Larix from sedimentary ancient DNA 4.3.5 Filtering of Illumina sequencing data and taxonomic assignments 4.3.6 Statistical analyses and visualization 4.3.7 Geochronology 4.4. Results 4.4.1 Overall composition of the DNA metabarcoding data 4.4.2 Terrestrial vegetation composition 4.4.2.1 Core L14-02: Late Pleistocene Yedoma Ice Complex 4.4.2.2 L14-03: Deeper late Pleistocene deposits 4.4.2.3 L14-04 Thermo terrace including Eemian deposits 4.4.2.4 Core L14-05: Alas with Holocene lake deposits and taberits of the Yedoma Ice Complex 4.4.2.5 The multivariate structure of the terrestrial vegetation among samples and cores 4.4.3 Genetic variation ofsediment-derived Larix sequences 4.5 Discussion 4.5.1 Tree taxa in the sedaDNA record - where do they come from? 4.5.2 Terrestrial plant community changes of warm phases since the last interglacial 4.5.3 Past genetic diversity of larch populations on Bol'shoy Lyakhovsky Island 4.6 Conclusion 4.7 Acknowledgements Chapter 5 5. Synopsis 5.1 The proxy potential of sedaDNA in paleobotanical reconstructions from sedimentary deposits 5.1.1 Combining sedaDNA and pollen to assess plant diversity and vegetation composition 5.1.2 Current limits and opportunities of sedaDNA approaches 5.2 Using genomic data to trace modern and past treeline dynamics 5.2.1 Modern genomic variation at the Siberian treeline 5.2.2 PCR-based markers for paleoenvironmental genetics 5.3 Terrestrial plant community changes and treeline dynamics in north-eastern Siberia since the last interglacial 5.3.1 Vegetation changes in north-eastern Siberia since the last interglacial 5.3.2 Implications for treeline dynamics 5.4 Conclusion 5.5 Outlook Appendix 1. Supplementary material for Manuscript I (Chapter 2) 2. Supplementary material for Manuscript II (Chapter 3) 3. Supplementary material for Manuscript III (Chapter 4) References Acknowledgements Erklärung