| 1. |
- Skoglund, Pontus
(author)
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Reconstructing the Human Past using Ancient and Modern Genomes
- 2013
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Doctoral thesis (other academic/artistic)abstract
- The study of DNA variation is one of the most promising avenues for learning about the evolutionary and historical past of humans and other species. However, the difficulty associated with obtaining DNA directly from ancient remains have for long kept genomic studies of population history trapped in time; confined to interpreting patterns of modern-day variation without direct historical observations. In this thesis, I outline new approaches for the retrieval, analysis and interpretation of large-scale genomic data from ancient populations, including solutions to overcome problems associated with limited genome coverage, modern-day contamination, temporal differences between samples, and post-mortem DNA damage. I integrate large-scale genomic data sets from ancient remains with modern-day variation to trace the human past; from traits targeted by natural selection in the early ancestors of anatomically modern humans, to their descendants' interbreeding with archaic populations in Eurasia and the spread of agriculture in Europe and Africa. By first reconstructing the earliest population diversification events of early modern humans using a novel large-scale genomic data set from Khoe-San populations in southern Africa, I devise a new approach to search for genomic patterns of selective sweeps in ancestral populations and report evidence for skeletal development as a major target of selection during the emergence of early modern humans. Comparing publicly available genomes from archaic humans, I further find that the distribution of archaic human ancestry in Eurasia is more complex than previously thought. In the first direct genomic study of population structure in prehistoric populations, I demonstrate that individuals associated with farming- and hunter-gatherer complexes in Neolithic Scandinavia were strongly genetically differentiated, and direct comparisons with modern-day populations as well as other prehistoric individuals from Southern Europe suggest that this structure originated from Northward expansion of Neolithic farming populations. Finally, I develop a bioinformatic approach for removing modern-day contamination from large-scale ancient DNA sequencing data, and use this method to reconstruct the complete mitochondrial genome sequence of a Siberian Neandertal that is affected by substantial modern-day contamination.
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| 2. |
- Jakobsson, Mattias, 1981-
(author)
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Monte Carlo Studies of Charge Transport Below the Mobility Edge
- 2012
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Doctoral thesis (other academic/artistic)abstract
- Charge transport below the mobility edge, where the charge carriers are hopping between localized electronic states, is the dominant charge transport mechanism in a wide range of disordered materials. This type of incoherent charge transport is fundamentally different from the coherent charge transport in ordered crystalline materials. With the advent of organic electronics, where small organic molecules or polymers replace traditional inorganic semiconductors, the interest for this type of hopping charge transport has increased greatly. The work documented in this thesis has been dedicated to the understanding of this charge transport below the mobility edge.While analytical solutions exist for the transport coefficients in several simplified models of hopping charge transport, no analytical solutions yet exist that can describe these coefficients in most real systems. Due to this, Monte Carlo simulations, sometimes described as ideal experiments performed by computers, have been extensively used in this work.A particularly interesting organic system is deoxyribonucleic acid (DNA). Besides its overwhelming biological importance, DNA’s recognition and self-assembly properties have made it an interesting candidate as a molecular wire in the field of molecular electronics. In this work, it is shown that incoherent hopping and the Nobel prize-awarded Marcus theory can be used to describe the results of experimental studies on DNA. Furthermore, using this experimentally verified model, predictions of the bottlenecks in DNA conduction are made.The second part of this work concerns charge transport in conjugated polymers, the flagship of organic materials with respect to processability. It is shown that polaronic effects, accounted for by Marcus theory but not by the more commonly used Miller-Abrahams theory, can be very important for the charge transport process. A significant step is also taken in the modeling of the off-diagonal disorder in organic systems. By taking the geometry of the system from large-scale molecular dynamics simulations and calculating the electronic transfer integrals using Mulliken theory, the off-diagonal disorder is for the first time modeled directly from theory without the need for an assumed parametric random distribution.
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| 3. |
- McKenna, James, 1987-
(author)
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Divergence, admixture and continuity in the human past : Demographic inference using ancient and modern genomes
- 2022
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Doctoral thesis (other academic/artistic)abstract
- Demographic forces shaping the genetic variation we observe today can include population divergences, admixture events and continuity through time. The advancement of high-throughput sequencing technologies, together with developments in molecular and bio-informatics methods, mean the number of ancient genomes available for inference has risen steeply. To make effective use of aDNA however, inference tools need to be developed that account for temporal as well as geographic sampling of genomes. Here I have developed, evaluated and applied methods for estimating divergence times between ancient and modern populations. I used simulation to study the sensitivity of these approaches to violations of model assumptions, before applying them to study the history of population divergence between pairs of populations from a global panel. Non-tree-like demography is common in the human past, with evidence of ancestral structure in the form of archaic admixture in the genomes of all non-African modern humans. Using SNP-array data collected from 118 ethnic groups in the Philippines, I show that the highest levels of Denisovan ancestry are found among the Ayta Magbukon, further highlighting the complex history between modern human groups and the archaic hominins occupying Eurasia before our arrival. Among the most important contributions population genetics has made to the study of the human past is the demonstration that cultural transitions and spread of technologies were often associated with migrating groups of people. This can result in the admixture, displacement or replacement of populations, and aDNA provides us with the opportunity to assess these trends directly through time. I developed a statistical tool to detect population continuity through time, evaluating its performance using simulation. Applied to a dataset of ancient genomes from Early Neolithic Scandinavia, I demonstrate population continuity in the hunter-gathering Pitted Ware culture, despite these people overlapping both geographically and temporally with farmers of the Funnel Beaker culture. In another study of the hunter-gatherer ancestors of the San people of southern Africa, I show evidence that this group exhibited long-term population isolation, remaining unaffected by admixture from outside southern Africa until surprisingly recent times. Using these ancient genomes, I provide further evidence that all modern Khoe-San populations exhibit significant levels of admixture with people of non-Khoe-San ancestry, demonstrating the strong impact migrations in this region have had in the past ~2,000 years.
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| 4. |
- Peyroteo-Stjerna, Rita, 1977-, et al.
(author)
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Multidisciplinary investigation reveals an individual of West African origin buried in a Portuguese Mesolithic shell midden four centuries ago
- 2022
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In: Journal of Archaeological Science. - : Elsevier. - 2352-409X .- 2352-4103. ; 42
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Journal article (peer-reviewed)abstract
- Cabeço da Amoreira is a well-studied shell midden with a robust chronology based on a large number ofradiocarbon dates on Mesolithic human burials. Surprisingly, we discovered one individual that lived about 400years ago buried in this site. We employed a multidisciplinary approach integrating archaeology, historical records,genetics, radiocarbon dating and stable isotope analysis to investigate the biogeographic origins of thisindividual and burial circumstances. We could determine that this was a man of West African origin, probablyfrom Senegambia, arriving in Portugal via the Trans-Atlantic Slave Trade. Our study provides new insights intoaspects of the life and death of a first-generation African individual in Portugal during the Trans-Atlantic SlaveTrade period and highlights the power of multidisciplinary research to unravel unwritten history.
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