Abstract
This PhD thesis examines the potential of describing biodiversity of green plants (Viridiplantae), birds (Aves) and mammals (Mammalia), in the context of next-generation sequencing, from the DNA that all organisms segregate into the environment (eDNA). The research is based on case studies of species assemblages described by eDNA recovered from contemporary surface soil and Holocene sediment sequences, to assess the accuracy and limitations of the approach. Biodiversity incorporates two aspects of ecological communities, including both the taxonomic richness and abundance of individual taxa. The main objectives of this thesis are describing technical and biological factors affecting perceived taxonomic richness and abundance, using metabarcoding coupled with nextgeneration sequencing of eDNA.
In chapter one, a study is designed to investigate the spatial deposition patterns of eDNA from mammals and birds in surface soil, originating form exotic animals. These settings provide a unique framework for testing the sensitivity and reliability of species identifications against known parameters, such as population census size, introduction period and behavioural peculiarities.
In chapter two, is a review of the progression in studies concerning sub-fossil plant DNA
(ancient DNA), with special emphasis on communication this information to non-geneticists, and is thought as a manual for use when collecting relevant archeobotanical sample material, with aim for later ancient DNA analysis.
In chapter three, a study is designed to test the performance of alternative DNA extraction protocols, in order to maximise DNA yields from plant macrofossils. Furthermore, the precision and efficiency of PCR amplification of ancient DNA is tested for alternative DNA polymerase enzymes, under influence of PCR inhibition.
In chapter four, alternative DNA extraction protocols and pipelines for characterising plant
eDNA are tested on samples from contrasting environments including modern, Holocene and Pleistocene sediment samples. These results are compared to pollen and macrofossil records described from earlier studies, creating a benchmark for comparing individual taxonomic assignment approaches.
In the appendix is found four articles, which were submitted and published during my PhD study period and are related to the work presented in the first four chapters. However, they are not included in the main manuscript, since my contribution to these articles has been minimal with regards to characterizing the reported DNA findings.
In chapter one, a study is designed to investigate the spatial deposition patterns of eDNA from mammals and birds in surface soil, originating form exotic animals. These settings provide a unique framework for testing the sensitivity and reliability of species identifications against known parameters, such as population census size, introduction period and behavioural peculiarities.
In chapter two, is a review of the progression in studies concerning sub-fossil plant DNA
(ancient DNA), with special emphasis on communication this information to non-geneticists, and is thought as a manual for use when collecting relevant archeobotanical sample material, with aim for later ancient DNA analysis.
In chapter three, a study is designed to test the performance of alternative DNA extraction protocols, in order to maximise DNA yields from plant macrofossils. Furthermore, the precision and efficiency of PCR amplification of ancient DNA is tested for alternative DNA polymerase enzymes, under influence of PCR inhibition.
In chapter four, alternative DNA extraction protocols and pipelines for characterising plant
eDNA are tested on samples from contrasting environments including modern, Holocene and Pleistocene sediment samples. These results are compared to pollen and macrofossil records described from earlier studies, creating a benchmark for comparing individual taxonomic assignment approaches.
In the appendix is found four articles, which were submitted and published during my PhD study period and are related to the work presented in the first four chapters. However, they are not included in the main manuscript, since my contribution to these articles has been minimal with regards to characterizing the reported DNA findings.
| Original language | Danish |
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| Publisher | Natural History Museum of Denmark, Faculty of Science, University of Copenhagen |
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| Number of pages | 257 |
| Publication status | Published - 2014 |