TY - BOOK
T1 - Improving High-Throughput Sequencing Approaches for Reconstructing the Evolutionary Dynamics of Upper Paleolithic Human Groups
AU - Seguin-Orlando, Andaine
PY - 2016
Y1 - 2016
N2 - In the last 10 years, ancient DNA research has experienced not less than a true revolution. Researchers are no longer limited to the sole characterization of short fragments of mitochondrial DNA, but can target complete genomes starting from less than a gram of osseous material. This revolution has been mainly driven by the development of High-Throughput DNA Sequencing (HTS) technologies but also by the implementation of novel molecular tools tailored to the manipulation of ultra short and damaged DNA molecules. Our ability to retrieve traces of genetic material has tremendously improved, pushing the time barrier for DNA analyses backwards into the Middle Pleistocene, and allowing for the characterization of genome-scale data from hundreds of individuals in a cost-effective manner. These datasets help researchers following how populations expanded their native range to unprecedented levels, replacing or admixing with other populations, including archaic hominins. Beyond the sole genomic sequence information, it is now possible to retrieve epigenetic marks, providing the first insights at how the regulation of gene expression changed in evolutionary times. In this thesis, we present the development and testing of innovative molecular approaches aiming at improving the amount of informative HTS data one can recover from ancient DNA extracts. We have characterized important ligation and amplification biases in the sequencing library building and enrichment steps, which can impede further ancient DNA analyses and should thus be considered when planning ancient genome sequencing. Additionally, we have tested a probe-free methylation-based capture approach aimed at enriching ancient extracts in methylated mammal DNA and characterized important experimental factors, including DNA degradation, that impact on the overall efficacy of the method. In a second part, we implemented some of these molecular tools to the processing of five Upper Paleolithic human samples from the Kostenki and Sunghir sites in Western Eurasia, in order to reconstruct the deep genomic history of European populations. The genome of Kostenki 14 enabled the dating of the admixture between Anatomically Modern Humans and Neanderthals some 54,000 years ago, and supported the hypothesis of a genomic continuity in Europe since the last 36,000 years. The analysis of the genomes of the four Sunghir individuals confirmed earlier work on admixture events between Neanderthals and anatomically modern humans and but also suggested that the latter were organized in small family units whose members avoided inbreeding.
AB - In the last 10 years, ancient DNA research has experienced not less than a true revolution. Researchers are no longer limited to the sole characterization of short fragments of mitochondrial DNA, but can target complete genomes starting from less than a gram of osseous material. This revolution has been mainly driven by the development of High-Throughput DNA Sequencing (HTS) technologies but also by the implementation of novel molecular tools tailored to the manipulation of ultra short and damaged DNA molecules. Our ability to retrieve traces of genetic material has tremendously improved, pushing the time barrier for DNA analyses backwards into the Middle Pleistocene, and allowing for the characterization of genome-scale data from hundreds of individuals in a cost-effective manner. These datasets help researchers following how populations expanded their native range to unprecedented levels, replacing or admixing with other populations, including archaic hominins. Beyond the sole genomic sequence information, it is now possible to retrieve epigenetic marks, providing the first insights at how the regulation of gene expression changed in evolutionary times. In this thesis, we present the development and testing of innovative molecular approaches aiming at improving the amount of informative HTS data one can recover from ancient DNA extracts. We have characterized important ligation and amplification biases in the sequencing library building and enrichment steps, which can impede further ancient DNA analyses and should thus be considered when planning ancient genome sequencing. Additionally, we have tested a probe-free methylation-based capture approach aimed at enriching ancient extracts in methylated mammal DNA and characterized important experimental factors, including DNA degradation, that impact on the overall efficacy of the method. In a second part, we implemented some of these molecular tools to the processing of five Upper Paleolithic human samples from the Kostenki and Sunghir sites in Western Eurasia, in order to reconstruct the deep genomic history of European populations. The genome of Kostenki 14 enabled the dating of the admixture between Anatomically Modern Humans and Neanderthals some 54,000 years ago, and supported the hypothesis of a genomic continuity in Europe since the last 36,000 years. The analysis of the genomes of the four Sunghir individuals confirmed earlier work on admixture events between Neanderthals and anatomically modern humans and but also suggested that the latter were organized in small family units whose members avoided inbreeding.
UR - https://rex.kb.dk/primo-explore/fulldisplay?docid=KGL01010158039&context=L&vid=NUI&search_scope=KGL&tab=default_tab&lang=da_DK
M3 - Ph.D. thesis
BT - Improving High-Throughput Sequencing Approaches for Reconstructing the Evolutionary Dynamics of Upper Paleolithic Human Groups
PB - Natural History Museum of Denmark, Faculty of Science, University of Copenhagen
ER -