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URI [dataset] University of Southampton Faculty of Environmental and Life Sciences Geography and Environmental Science Late-Quaternary Dynamics of Northern Plant Communities: A Sedimentary Ancient DNA (SedaDNA) Perspective by Charlotte Louise Clarke ORCID ID 0000-0002-1296-2229 Thesis for the degree of Doctor of Philosophy (Ph.D.) September 2019 University of Southampton Abstract Faculty of Environmental and Life Sciences Geography and Environmental Science Thesis for the degree of Doctor of Philosophy (Ph.D.) Late-Quaternary Dynamics of Northern Plant Communities: A Sedimentary Ancient DNA (SedaDNA) Perspective by Charlotte Louise Clarke Tundra plant communities in the northern high latitudes are expected to undergo large distributional changes, habitat loss and/or local species extinction with future climate changes. This is in part linked to the projected northward expansion of climate-sensitive, woody plant taxa of the boreal forest-tundra ecotone. Nevertheless, recurrent glacial-interglacial cycles throughout the Quaternary period (<2.6 million years BP) have repeatedly shifted the ranges of many northern plants. Knowledge of how the composition of plant communities changed in response to previous large-magnitude climate changes could therefore inform predictive modelling of the effect of global change on their distributions. Ancient DNA recovered from sediments (sedaDNA) has proved a useful new tool for studying change in terrestrial ecosystems over time. The cold climate conditions in northern regions appear to be ideal for the long-term preservation of extra-cellular (i.e. “environmental”) DNA. This thesis explores the potential of sedaDNA extracted from lake sediments for reconstructing changes in the composition and diversity of northern plant communities since the peak of last glacial interval (ca. 24,000 cal. years BP). It focuses on three specific northern regions: a previously glaciated area of northeast Norway and two regions (the Polar Ural Mountains of northern Russia and interior Alaska) which remained ice-free during the last glacial interval. In each of the four papers presented in this thesis, the analysis of sedaDNA is shown to contribute new insights towards understanding the long-term dynamics of northern plant communities over the late-Quaternary interval. Many of these new insights arise from unique differences in the source and representation of sedaDNA compared to records derived from pollen. Reconstructions of community composition and floristic richness were improved by using sedaDNA as the sedaDNA signal is less sensitive to “swamping” by woody anemophilous taxa at the expense of insect-pollinated herbaceous taxa than pollen. SedaDNA was also able to document fossil-silent plant taxa which are poorly represented and/or taxonomically resolved within pollen records, including the coniferous tree Larix, a diversity of arctic-alpine herbs and turnover amongst bryophyte and grass genera over time. The findings presented in this thesis demonstrate that lake selection is an important consideration for plant sedaDNA studies, as it acts as a control on levels of DNA preservation, detection success and representation of floristic composition. At a small lake (with <2 km2 catchment area) located close to the Pinus treeline in northeast Norway, the sedaDNA record shows little change in floristic composition and diversity over the Holocene period investigated (ca. 10,700 and 3,300 cal. years BP), with high values of Pinus sedaDNA detected throughout the record. The high Pinus values could not be determined with certainty as representing past local presence of the tree. In contrast, at a large lake (with >200 km2 catchment) in the Polar Urals, located north of a treeline comprising Larix and Picea, the sedaDNA record documents a range of different plant communities growing within its large and topographically complex catchment, including a period of establishment of coniferous forest taxa between ca. 9000 and 4000 cal. years BP. Contrary to the conclusions of earlier sedaDNA studies, the findings presented in Paper III demonstrate that when compared with a detailed pollen record counted with a high pollen sum, sedaDNA and pollen analyses can show considerable overlap in the pattern of occurrence of key plant taxa. At the two sites which remained unglaciated during the last glacial interval, the sedaDNA records reveal a diverse full-glacial flora of what can best be called a herb-tundra vegetation, dominated by forbs (e.g. Papaver, Draba, Saxifraga sp., Astragalus, Bistorta vivipara) with some graminoids (e.g. Puccinellia, Festuca, Juncus biglumis, Bromus pumpellianus). Floristic richness based on sedaDNA at these sites showed a sustained increase until the early- to middle-Holocene, with the sequential addition of new plant taxa over time, before stabilising over the later Holocene. The sedaDNA record from the previously glaciated site in northeast Norway provides no evidence for increased floristic richness over time that might have been expected due to successional arrival and/or delayed immigration of species. Lastly, the sedaDNA record from the site in the Polar Urals provides robust evidence of persistence of arctic-alpine taxa through several large-magnitude climate changes over the past 24,000 cal. years BP, demonstrating the buffering capacity of a spatially heterogeneous mountain region. However, a distinct decline in their proportional abundance and diversity began as soon as woody taxa started to expand, suggesting that in a future warming scenario, local species loss may occur long before tree establishment occurs. Table of Contents Table of Contents Table of Contents ............................................................................................................ i Table of Tables .............................................................................................................. vii Table of Figures .............................................................................................................. ix Research Thesis: Declaration of Authorship ................................................................... xv Acknowledgements ..................................................................................................... xvii Chapter 1 Introduction ................................................................................................ 1 1.1 Preamble .................................................................................................................. 1 1.2 The Last Glacial-Interglacial Transition .................................................................... 1 1.3 Compositional Changes in Northern Plant Communities Over the Last Glacial- Interglacial Transition .............................................................................................. 3 1.4 Research Questions ................................................................................................. 5 1.5 Research Aim and Objectives ................................................................................... 6 1.6 Thesis Structure and Author Contributions .............................................................. 6 Chapter 2 Literature Review .......................................................................................11 2.1 Introduction ........................................................................................................... 11 2.2 Present-Day Patterns in the Diversity and Distribution of Northern Plant Communities .......................................................................................................... 11 2.3 Floristic Changes Over the Last Glacial-Interglacial Cycle....................................... 14 2.3.1 The Last Glacial Maximum (LGM) ................................................................... 14 2.3.2 Postglacial Colonisation and Development of Plant Communities Within Previously Glaciated Regions ......................................................................... 15 2.3.3 Composition of the Full-Glacial Flora Within Ice-Free (i.e. Unglaciated) Regions........................................................................................................... 16 2.3.4 Traditional Palaeoecological Records ............................................................. 18 2.4 Sedimentary Ancient DNA (SedaDNA) Analysis ...................................................... 18 2.4.1 A Brief History of Ancient DNA (aDNA) .......................................................... 18 2.4.2 Environmental DNA (eDNA) ..........................................................................