| 1. |
- Ausmees, Kristiina
(författare)
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Methodology and Infrastructure for Statistical Computing in Genomics : Applications for Ancient DNA
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis concerns the development and evaluation of computational methods for analysis of genetic data. A particular focus is on ancient DNA recovered from archaeological finds, the analysis of which has contributed to novel insights into human evolutionary and demographic history, while also introducing new challenges and the demand for specialized methods.A main topic is that of imputation, or the inference of missing genotypes based on observed sequence data. We present results from a systematic evaluation of a common imputation pipeline on empirical ancient samples, and show that imputed data can constitute a realistic option for population-genetic analyses. We also develop a tool for genotype imputation that is based on the full probabilistic Li and Stephens model for haplotype frequencies and show that it can yield improved accuracy on particularly challenging data. Another central subject in genomics and population genetics is that of data characterization methods that allow for visualization and exploratory analysis of complex information. We discuss challenges associated with performing dimensionality reduction of genetic data, demonstrating how the use of principal component analysis is sensitive to incomplete information and performing an evaluation of methods to handle unobserved genotypes. We also discuss the use of deep learning models as an alternative to traditional methods of data characterization in genomics and propose a framework based on convolutional autoencoders that we exemplify on the applications of dimensionality reduction and genetic clustering.In genomics, as in other fields of research, increasing sizes of data sets are placing larger demands on efficient data management and compute infrastructures. The final part of this thesis addresses the use of cloud resources for facilitating data analysis in scientific applications. We present two different cloud-based solutions, and exemplify them on applications from genomics.
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| 2. |
- Björklund, Mattias, 1971-
(författare)
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Beyond Moral Teaching : Financial Literacy as Citizenship Education
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis explores what financial literacy is, what financial literacy becomes and what financial literacy could become within the context of a citizenship education such as the Swedish upper secondary subject of social studies. Financial literacy does not intuitively converge with social sciences which leaves social studies teachers to both teach and realise financial literacy. Thus, teachers become co-creators of financial literacy as a school subject. This thesis explores this process via two different studies resulting in four research articles. In the first study, semi-structured interviews – analysed through PCK – are used to explore the perceptions of Swedish social studies teachers in upper secondary school regarding financial literacy teaching and learning. The findings include differences between experienced and novice teachers regarding which content knowledge and pedagogical approaches they use. However, all teachers express difficulties fitting financial literacy into social studies, mainly due to a perception of financial literacy primarily being a private matter, along with the unclear relationship between financial and societal issues. The second study is designed as a financial literacy teaching intervention. Students’ views on a financial dilemma are analysed using citizenship conceptions and threshold concepts. The findings are used to discuss design principles for financial literacy teaching. Salient conclusions in the thesis include citizenship education being able to frame financial literacy and provide epistemic features which can make financial literacy more teachable and learnable. It is hoped that the results from this thesis can inform future financial literacy teaching design as well as policy discussion related to financial literacy teaching and learning contextualised with another subject, especially citizenship education.
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| 3. |
- Breton, Gwenna
(författare)
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Human demographic history : Insights on the human past based on genomes from Southern through Central Africa
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Evidence from paleontology, archaeology and population genetics support that modern humans originated in Africa. While the out-of-Africa event and subsequent colonization of all continents are well documented, human history in Africa at that time and before is less studied. Some current-day hunter-gatherer populations trace most of their genetic lineages to populations who inhabited Sub-Saharan Africa until the arrival of farming. They are informative about human history before and after the arrival of farming.I studied high-coverage genomes from two such groups, the Khoe-San from Southern Africa and the rainforest hunter-gatherers from Central Africa. I generated a total of 74 genomes, significantly increasing the number of genomes from Sub-Saharan African hunter-gatherers. I compared several versions of a commonly used pipeline for high-coverage genomes and showed that using standard ascertained reference datasets has no significant impact on variant calling in populations from Sub-Saharan Africa. Using the full genome information, I described the genetic diversity in the Khoe-San and in the rainforest hunter-gatherers and showed that gene flow from agropastoralist groups increased the Khoe-San genetic diversity. I also detected a signal of population size decline in the Khoe-San around the time of the out-of-Africa event, and I evaluated the power of the method to detect bottlenecks by applying it to simulated data. I investigated the history of modern humans in Africa by estimating divergence times between populations and applying an Approximate Bayesian Computation analysis. We confirmed that the earliest divergence event was between the Khoe-San ancestral lineage and the rest of modern humans, ~250-350 kya. I also showed that the possibility of high gene flow should be incorporated in models of human evolution.I furthermore examined SNP array data for two BaTwa populations from Zambia and showed that 20-30% of their autosomal diversity is hunter-gatherer-like. The estimated times for the admixture between a presumably local hunter-gatherer population and incoming agropastoralist groups are consistent with archaeological records.In this thesis, I investigated questions related to human history in Sub-Saharan Africa, from the emergence of modern humans ~300 kya to recent events related to the expansion of farming.
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| 4. |
- Coutinho, Alexandra
(författare)
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Where our feet have taken us : Examples of human contact, migration, and adaptation as revealed by ancient DNA
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In spite of our extensive knowledge of the human past, certain key questions remain to be answered about human prehistory. One involves the nature of cultural change in material culture through time from the perspective of how different ancient human groups interacted with one another. The other is how humans have adapted to the different environments as they migrated and populated the rest of the world from their origin in Africa. For my thesis I have investigated examples of human evolutionary history using genetic information from ancient human remains. Chapter 1 focused on the nature of possible interaction between the Pitted Ware Culture (PWC) and Battle Axe Culture (BAC) on the island of Gotland, in the Baltic Sea. Through the analysis of 4500 year old human remains from three PWC burial sites, I found that the existence of BAC influences in these burial sites was the result of cultural and not demic influence from the BAC. In chapter 2, I investigated the ancestry of a Late Stone Age individual from the southwestern Cape of South Africa. Population genetic analyses revealed that this individual was genetically affiliated with Khoe groups in southern Africa, a genetic make-up that is today absent from the Cape. Chapter 3 investigated the genetic landscape of prehistoric individuals from southern Africa. Specifically, I explored frequencies of adaptive variants between Late Stone Age and Iron Age individuals. I found an increase in disease resistance alleles in Iron Age individuals and attributed this to the effects of the Bantu expansion. Chapter 4 incorporated a wider range of trait-associated variants among a greater number of modern-day populations and ancient individuals in Africa. I found that many allele frequency patterns found in modern populations follow the routes of major migrations which took place in the African Holocene. The thesis attests to the complexity of human demographic history in general, and how migration contributes to adaptation by dispersing novel adaptive variants to populations.
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| 5. |
- Daskalaki, Evangelia
(författare)
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Archaeological Genetics - Approaching Human History through DNA Analysis
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- There are a variety of archaeological questions, which are difficult to assess by traditional archaeological methods. Similarly, there are genetic and population genetic questions about human evolution and migration that are difficult to assess by studying modern day genetic variation. Archaeological genetics can directly study the archaeological remains, allowing human history to be explored by means of genetics, and genetics to be expanded into historical and pre-historical times. Examples of archaeological questions that can be resolved by genetics are determining biological sex on archaeological remains and exploring the kinship or groups buried in close proximity. Another example is one of the most important events in human prehistory – the transition from a hunter-gatherer lifestyle to farming - was driven through the diffusion of ideas or with migrating farmers. Molecular genetics has the potential to contribute in answering all these questions as well as others of similar nature. However, it is essential that the pitfalls of ancient DNA, namely fragmentation, damage and contamination are handled during data collection and data analysis.Analyses of ancient DNA presented in this thesis are based on both mitochondrial DNA and nuclear DNA through the study of single nuclear polymorphisms (SNPs). I used pyrosequencing assays in order to identify the biological sex of archaeological remains as well as verifying if fragmented remains were human or from animal sources. I used a clonal assay approach in order to retrieve sequences for the HVRI of a small family-like burial constellation from the Viking age. By the use of low coverage shotgun sequencing I retrieved sequence data from 13 crew members from the 17th century Swedish man-of-war Kronan. This data was used to determine the ancestry of the crew, which in some cases was speculated to be of non-Scandinavian or non-European origin. However, I demonstrate that all individuals were of European ancestry. Finally, I retrieved sequence data from a Neolithic farmer from the Iberian Peninsula, which added one more facet of information in exploring the Neolithization process of Europe. The Neolithic Iberian individual was genetically similar to Scandinavian Neolithic farmers, indicating that the genetic variation of prehistoric Europe correlated with subsistence mode rather than with geography.
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| 6. |
- Fraser, Magdalena
(författare)
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People of the Dolmens and Stone Cists : An archaeogenetic Investigation of Megalithic Graves from the Neolithic Period on Gotland
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The study of ancient genomics of pre-historic human remains has in recent years offered unprecedented knowledge regarding pre-historic migration and population structure on the European continent which has fundamentally altered the current views in the archaeological community. However, the merging of the two fields, archaeology and genetics, is still in its infancy and much work is still needed in order for these fields to integrate. In this thesis I explore how genetic analyses, in combination with contextual radiocarbon dating and isotopic analyses for diet and mobility can be used to investigate demographic events on a local and regional level. This is done through the investigation of people buried in five previously excavated megalithic tombs on the Island of Gotland dated to the Neolithic period. I present the genomic population structure and archaeological background for the pre-historic European reference data and show how this is used to investigate population continuity, demographic shifts, cultural duality, and admixture for local and regional contexts. I present new data and explore the Strontium-baseline for the Gotland biosphere which is used for the mobility analyses. I show that mitochondrial haplogroup data is especially useful in combination with isotopic data, and radiocarbon dating for investigation of demographic shifts on a larger scale. I also show that genomic data gives unique insights into the individuals’ life history which, together with the established demographic background allows for fine scale investigation of population demographic events within and between different archaeological contexts. Finally I show that the different Neolithic contexts on Gotland to a large extent involves immigration of new groups to the island, and that the contextual breaks seen in the archaeological record during the Neolithic period are connected with cultural and population demographic shifts. This dissertation demonstrates that genomic analyses, in combination with archaeology and isotopic analyses, as well as contextual osteological analyses and radiocarbon dating, present unique insights into the life history of the actual people who lived the lives we try to understand.
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| 7. |
- Gattepaille, Lucie, 1984-
(författare)
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Population Genetic Methods and Applications to Human Genomes
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Population Genetics has led to countless numbers of fruitful studies of evolution, due to its abilities for prediction and description of the most important evolutionary processes such as mutation, genetic drift and selection. The field is still growing today, with new methods and models being developed to answer questions of evolutionary relevance and to lift the veil on the past of all life forms. In this thesis, I present a modest contribution to the growth of population genetics. I investigate different questions related to the dynamics of populations, with particular focus on studying human evolution. I derive an upper bound and a lower bound for FST, a classical measure of population differentiation, as functions of the homozygosity in each of the two studied populations, and apply the result to discuss observed differentiation levels between human populations. I introduce a new criterion, the Gain of Informativeness for Assignment, to help us decide whether two genetic markers should be combined into a haplotype marker and improve the assignment of individuals to a panel of reference populations. Applying the method on SNP data for French, German and Swiss individuals, I show how haplotypes can lead to better assignment results when they are supervised by GIA. I also derive the population size over time as a function of the densities of cumulative coalescent times, show the robustness of this result to the number of loci as well as the sample size, and together with a simple algorithm of gene-genealogy inference, apply the method on low recombining regions of the human genome for four worldwide populations. I recover previously observed population size shapes, as well as uncover an early divergence of the Yoruba population from the non-African populations, suggesting ancient population structure on the African continent prior to the Out-of-Africa event. Finally, I present a case study of human adaptation to an arsenic-rich environment.
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| 8. |
- Hammarén, Rickard, 1989-
(författare)
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From the migrations of herders and farmers to the colonial era and the modern-day : Genetic inferences on African demographic history
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Africa is the birthplace of the human species and home to great linguistic, cultural, and genetic diversity. Despite this, the genetics of the peoples of the continent remains understudied. In this thesis, I apply population genetic approaches, to contribute to the knowledge of human demographic history in Africa. Specifically, I investigated three events that have had major impacts on human population genetics in Africa. Paper I, investigated Eurasian back migrations into Northeast Africa and what genetic patterns this has left in the current-day populations of the area. I identified complex demography and linguistic stratification of Eurasian admixture in the region. These genetic patterns coincide in time with historical events such as the spread of Islam, the fall of the Kingdom of Aksum, and trade routes across the Red Sea. Paper II focused on the Bantu expansion, the different migratory routes of Bantu-speakers out of West Africa, and how they shaped the genetic makeup of the peoples of sub-equatorial Africa. We compiled the most comprehensive geographically distributed genetic dataset of Bantu-speaking individuals to date. I investigated the spatial patterns of migrations and the decline of genetic diversity from their homeland. I find evidence for serial founder events and migrations across Zambia and the Congo basin to the rest of sub-equatorial Africa. Paper III and IV involved South Africa and the effects that European colonialism and 20:th century policies have had on the country's genetic landscape. Paper III focuses on the Afrikaner population of South Africa, descendants of the first European settlers of the Cape colony, I describe the extent of African and Asian admixture in this population and investigate evidence of selection and adaptive admixture. Paper IV focuses on the Coloured population of South Africa, an emergent cultural identity. The Coloured population traces their origin primarily to Khoe-San women, manumitted slaves, and European men from the Cape colony. The term Coloured was also used for admixed individuals under the Apartheid racial classification system. The Coloured has one of the most complex admixture histories in the world, with genetic ancestry from Europe, East and South Asia, West and East Africa, as well as southern African Khoe-San. In our paper, we describe these complex patterns, the differences in sex-biased admixture, and determine the admixture dates across an extensive collection of Coloured, across South Africa. My work thus highlights complex genetic patterns within African human demographic history and shows how profoundly it has been shaped by the movement of people in the last 5 000 years.
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| 9. |
- Hollfelder, Nina, 1985-
(författare)
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Population genetic history and patterns of admixture : Examples from northeastern and southern Africa
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The origin of humans lies in Africa, as has been shown by archaeology, paleontology and genetics. Here, we can find the largest genetic diversity and the deepest split among human populations. African genetic diversity has been shaped by a long and complex history. In this thesis, I applied population genomic methods to investigate different aspects of the demographic history of Africa, specifically northeast and southern Africa.Both of these regions are population melting-pots, with many historically known major migrations.In northeast African populations, Eurasian admixture in central, northern, and eastern Sudanese populations was identified to be of Middle Eastern origin and the admixture time coincides with the Arab expansion. In northeast Africa I also studied alleles associated with lactase persistence, the ability to digest milk at an adult age. A wide diversity of these alleles was detected in Sudan, most commonly among pastoralists. The presence of a Middle Eastern LP-allele and absence of a European LP-allele is consistent with the admixture pattern observed in the first paper.I deciphered the patterns of genetic admixture in the Afrikaner population of South Africa and compared admixture patterns of the X-chromosome and autosomes to disentangle sex-biased admixture in southern African populations.The Afrikaner were shown to carry on average 5% non-European admixture, mostly from Khoe-San, East and South Asian sources. The admixture was sex-biased, with larger contributions from European males and admixture with Africans can be dated to 9-10 generations ago – fitting previous genealogical estimates of the age and the history of the population.Bantu-speaker/Khoe-San contact shows a pattern of female Bantu-speaker bias, which is conflicting with previous mtDNA and Y-chromosome studies. A change in mate-choice over time could explain this discrepancy.This thesis contributes to a deeper understanding of African demographic history in general and of some previously understudied populations and geographic areas in particular.
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| 10. |
- Jakobsson, Erik, 1987-
(författare)
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Condition Monitoring in Mobile Mining Machinery
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The global mining industry is currently facing a huge transition from manually operated individual vehicles, to autonomous vehicles being part of an industrial process-like environment. The change is driven by the never ending need for efficient, safe, and environmentally friendly operations. One intentional consequence is an increased distance between the operator, and the machine being operated. This enables safer working environments and reduced cost for ventilation and other supporting systems in a mine, but it also results in the loss of the systems most important sensor. The transition from manual to autonomous operation requires this gap to be filled from a system awareness perspective, which lately has become evident with the large resources that car manufacturers use to develop self-driving cars. This thesis also targets system awareness, but of the internal kind. By this we mean knowing the condition of the machine and its capabilities. The operator is the most important sensor also for internal condition, and if no operator is present on the machine, this gap needs to be filled.The mining industry is categorized by small series and significant customization of machinery. This is a direct result of the geological prerequisites, where differently shaped ore bodies cause large differences in mine layout and mining methods. This thesis explores how methods estimating the health of mining vehicles can be used in this setting, by utilizing sensor signals to make assessments of the current vehicle condition and tasks.The resulting health information can be used both to aid in tasks such as maintenance planning, but also as an important input to decision making for the planning system, i.e. how to run the vehicle for minimum wear and damage, while maintaining other mission objectives.Two applications are studied. Mine trucks have slow degradation modes, such as crack propagation and fatigue, that are difficult to handle with data driven approaches since data collection requires significant amounts of time. A contribution in this thesis, is a method to utilize short term measurement data together with data driven methods to obtain the loads of a vehicle, and then to use physics based approaches to estimate the actual damage.The second application considers monitoring faults in hydraulic rock drills using online measurements during operation. The rock drill is a specifically difficult case, since severe vibration levels limits the locations and types of sensors that can be used. The main contribution is a method to handle individual differences when classifying internal faults using a single pressure sensor on the hydraulic supply line. A complicating factor is the large influence of wave propagation, causing different individuals to show different behavior.
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