Novel approaches to reconstructing complex ecosystems : studies on modern and ancient sedimentary DNA in Upper Lake Constance

Abstract

Fifteen to eleven thousand years ago, the Earth transitioned from the Pleistocene to the Holocene through a series of post-glacial climate fluctuations. This change of climate reshaped the biosphere and likely triggered the invention and spread of agriculture among human societies, marking the advent of global anthropogenic ecosystem transformation. Ecological changes in the Holocene, especially on human-populated land, have been described in paleoecological and archaeological research as incessant and having complicated causes of natural and anthropogenic origin. Conventionally, these changes are demonstrated through the presence and abundance of fossil remains and reduced to diversity or distance metrics. Due to methodological constraints, dynamics of a wider breath of organisms as a result of interaction in the same space and time are rarely described. This thesis attempts to reconstruct a regional ecological history since the end of the Pleistocene by examining organisms across domains of life. The study system, Lake Constance, came into being at the end of the last glacial period and its rich archeological record bear witness to millennial old occupation of its shores . The environmental changes it has sustained are characterised through shotgun-sequenced sedimentary ancient DNA, a relatively young type of paleoecological data that is ecological in its own genesis. The first research study of this thesis therefore links the distribution of sedimentary DNA to the organisms’ presence in their natural habitat and additionally shows that sedimentary DNA reflects the work of hydrological activities on local terrain. The second research study brings focus to the dynamics of the prokaryote life and their sensitive responses to environmental changes, which manifest not only through the expansion of lineages related to human livelihood in recent centuries, but potentially also the genetic changes of aquatic microbes persisting in the lake for thousands of years. The last research study concerns the collective changes of eukaryotes, including plants, phytoplankton, fungi and animals. I show that community changes, such as succession, turnover and change in biomass, have distinct patterns in different times and are not always in synchrony across species. In the course of Lake Constance’s history, no organisms stood unaffected under the forces of nature and human.