TY - BOOK

T1 - Paleo-Environmental Reconstruction Using Ancient DNA

AU - Pedersen, Mikkel Winther

PY - 2016

Y1 - 2016

N2 - The aim of this thesis has been to investigate and expand the methodology and applicability forusing ancient DNA deposited in lake sediments to detect and determine its genetic sources forpaleo-environmental reconstruction. The aim was furthermore to put this tool into an applicablecontext solving other scientifically interesting questions. Still in its childhood, ancientenvironmental DNA research has a large potential for still developing, improving and discoveringits possibilities and limitations in different environments and for identifying various organisms,both in terms of the sampling methods and strategies (taphonomic processes), the more fundamentalmolecular methodologies (e.g. extraction and sequencing) and eventually the bioinformaticprocessing. In the enclosed studies we have tried to take some principal steps towards improvingthis, 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) forreconstructing floristic history. In prolongation of the results obtained in paper 2 we developed aholistic metagenomic method combined with shotgun sequencing of ancient DNA in lake sedimentsamples to reconstruct organismal assemblages in addition to the flora e.g. micro-, meso- andmegafauna, fungi and microbial communities (Paper 3). Fundamental processes were tested, using ahistorical record from the botanical garden in the centre of Copenhagen (Paper 4), by comparingthis high resolution sediment archive to the historical sources about the anthropogenic activity anddisease history. Similarly, we investigated the flora and faunal content of ancient midden depositsfrom the four distinct Greenlandic cultures over the past 4,000 cal. yrs BP, to investigate theapplicability of the molecular record as a supplementary tool to reconstruct the cultures resourceeconomies (Paper 5). Lastly, we felt it was timely for a focused review paper summarizing the pastdecade of research and addressing the future perspectives for paleo-environment reconstructionusing ancient DNA from lake sediment records (Paper 6). The main emphasis in the review is puton 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 mymain focus. They, however, still contain important analysis and results that provide pieces to thecomplete picture of this thesis and are therefore appended..

AB - The aim of this thesis has been to investigate and expand the methodology and applicability forusing ancient DNA deposited in lake sediments to detect and determine its genetic sources forpaleo-environmental reconstruction. The aim was furthermore to put this tool into an applicablecontext solving other scientifically interesting questions. Still in its childhood, ancientenvironmental DNA research has a large potential for still developing, improving and discoveringits possibilities and limitations in different environments and for identifying various organisms,both in terms of the sampling methods and strategies (taphonomic processes), the more fundamentalmolecular methodologies (e.g. extraction and sequencing) and eventually the bioinformaticprocessing. In the enclosed studies we have tried to take some principal steps towards improvingthis, 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) forreconstructing floristic history. In prolongation of the results obtained in paper 2 we developed aholistic metagenomic method combined with shotgun sequencing of ancient DNA in lake sedimentsamples to reconstruct organismal assemblages in addition to the flora e.g. micro-, meso- andmegafauna, fungi and microbial communities (Paper 3). Fundamental processes were tested, using ahistorical record from the botanical garden in the centre of Copenhagen (Paper 4), by comparingthis high resolution sediment archive to the historical sources about the anthropogenic activity anddisease history. Similarly, we investigated the flora and faunal content of ancient midden depositsfrom the four distinct Greenlandic cultures over the past 4,000 cal. yrs BP, to investigate theapplicability of the molecular record as a supplementary tool to reconstruct the cultures resourceeconomies (Paper 5). Lastly, we felt it was timely for a focused review paper summarizing the pastdecade of research and addressing the future perspectives for paleo-environment reconstructionusing ancient DNA from lake sediment records (Paper 6). The main emphasis in the review is puton 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 mymain focus. They, however, still contain important analysis and results that provide pieces to thecomplete picture of this thesis and are therefore appended..

UR - https://soeg.kb.dk/permalink/45KBDK_KGL/fbp0ps/alma99122559631005763

M3 - Ph.D. thesis

BT - Paleo-Environmental Reconstruction Using Ancient DNA

PB - Natural History Museum of Denmark, Faculty of Science, University of Copenhagen

ER -