The aim of this thesis has been to investigate and expand the methodology and applicability for
using ancient DNA deposited in lake sediments to detect and determine its genetic sources for
paleo-environmental reconstruction. The aim was furthermore to put this tool into an applicable
context solving other scientifically interesting questions. Still in its childhood, ancient
environmental DNA research has a large potential for still developing, improving and discovering
its possibilities and limitations in different environments and for identifying various organisms,
both in terms of the sampling methods and strategies (taphonomic processes), the more fundamental
molecular methodologies (e.g. extraction and sequencing) and eventually the bioinformatic
processing. In the enclosed studies we have tried to take some principal steps towards improving
this, firstly by reviewing previous research on ancient and modern environmental DNA (Paper 1),
secondly by setting up a comparative study (Paper 2) to investigate how an ancient plant DNA
(mini)-barcode can reflect other traditional methods (e.g. pollen and macrofossils) for
reconstructing floristic history. In prolongation of the results obtained in paper 2 we developed a
holistic metagenomic method combined with shotgun sequencing of ancient DNA in lake sediment
samples to reconstruct organismal assemblages in addition to the flora e.g. micro-, meso- and
megafauna, fungi and microbial communities (Paper 3). Fundamental processes were tested, using a
historical record from the botanical garden in the centre of Copenhagen (Paper 4), by comparing
this high resolution sediment archive to the historical sources about the anthropogenic activity and
disease history. Similarly, we investigated the flora and faunal content of ancient midden deposits
from the four distinct Greenlandic cultures over the past 4,000 cal. yrs BP, to investigate the
applicability of the molecular record as a supplementary tool to reconstruct the cultures resource
economies (Paper 5). Lastly, we felt it was timely for a focused review paper summarizing the past
decade of research and addressing the future perspectives for paleo-environment reconstruction
using ancient DNA from lake sediment records (Paper 6). The main emphasis in the review is put
on the floristic history, hereby reflecting the focus of the studies published.
Appending this thesis are three papers (paper 7-9) which are in review or published,
and which have been conducted during my time as a PhD student, although they have not been my
main focus. They, however, still contain important analysis and results that provide pieces to the
complete picture of this thesis and are therefore appended..