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1.
  • Säll, T., et al. (creator_code:aut_t)
  • Chloroplast DNA indicates a single origin of the allotetraploid Arabidopsis suecica
  • 2003
  • record:In_t: Journal of Evolutionary Biology. - : John Wiley & Sons Inc.. - 1010-061X .- 1420-9101. ; 16:5, s. 1019-1029
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • DNA sequencing was performed on up to 12 chloroplast DNA regions [giving a total of 4288 base pairs (bp) in length] from the allopolyploid Arabidopsis suecica (48 accessions) and its two parental species, A. thaliana (25 accessions) and A. arenosa (seven accessions). Arabidopsis suecica was identical to A. thaliana at all 93 sites where A. thaliana and A. arenosa differed, thus showing that A. thaliana is the maternal parent of A. suecica. Under the assumption that A. thaliana and A. arenosa separated 5 million years ago, we estimated a substitution rate of 2.9 x 10(-9) per site per year in noncoding single copy sequence. Within A. thaliana we found 12 substitution (single bp) and eight insertion/deletion (indel) polymorphisms, separating the 25 accessions into 15 haplotypes. Eight of the A. thaliana accessions from central Sweden formed one cluster, which was separated from a cluster consisting of central European and extreme southern Swedish accessions. This latter cluster also included the A. suecica accessions, which were all identical except for one 5 bp indel. We interpret this low level of variation as a strong indication that A. suecica effectively has a single origin, which we dated at 20 000 years ago or more.
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2.
  • Ausmees, Kristiina (creator_code:aut_t)
  • Methodology and Infrastructure for Statistical Computing in Genomics : Applications for Ancient DNA
  • 2022
  • swepub:Mat_doctoralthesis_t (swepub:level_scientificother_t)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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3.
  • Olsson, Mattias, 1975, et al. (creator_code:aut_t)
  • Sorption of Pu(III-IV) onto TiO2: A Preliminary Study
  • 2003
  • record:In_t: Materials Research Society Symposium Proceedings. - 155899694X ; 757, s. 517-522
  • swepub:Mat_conferencepaper_t (swepub:level_refereed_t)abstract
    • A preliminary study of the sorption of reduced plutonium (III-IV) onto TiO2 has been done under anoxic conditions at varying pH and ionic strength. The first approach was to study tetravalent Pu, but the sorption decreases with time in this case. This is probably due to disproportionation of Pu(IV) at the TiO2 surface, which then acts as a catalyst. A further observation that supports this explanation is that the sorption of Pu(IV) onto the walls of the experimental equipment is in some cases higher than the sorption of (disproportioned) Pu onto the oxide.Pu(III) sorption onto the oxide was also investigated and showed similarities with the previously investigated sorption of Pm(III) in a similar system.
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4.
  • Olsson, Mattias, 1975, et al. (creator_code:aut_t)
  • Sorption of Pu(VI) onto TiO2
  • 2003
  • record:In_t: Journal of Colloid and Interface Science. ; 266:2, s. 269-275
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The sorption of Pu(VI) onto TiO2 was studied as a function of pH (210) and Pu concentration (10−810−4 M) under an N2 atmosphere, in 0.016 and 0.1 M NaClO4. A batch-wise method was used, in which pH was measured in separate experimental containers after removal of a sample to determine the amount of Pu that had been sorbed. As Pu is radioactive, it was used as a tracer and measured by liquid scintillation counting. No ionic strength dependence was discerned, which was taken as an indication of inner sphere complex formation. In the interval of pH 27 the system could be described by the formation of two positively charged surface complexes using a 1-pK Stern model. Sorption of the plutonyl ion (PuO22+) and the first hydrolysis species (PuO2(OH)+) was estimated using FITEQL to logK1=6.9 and logK2=1.4, respectively.
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5.
  • Olsson, Mattias, 1975, et al. (creator_code:aut_t)
  • Surface Charge Densities of Two Actinide(IV) Oxides: UO2 and ThO2
  • 2002
  • record:In_t: Journal of Colloid and Interface Science. - 1095-7103 .- 0021-9797. ; 256:2, s. 256-261
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The surface charge behavior of uranium(IV) oxide and thorium(IV) oxide was investigated by potentiometric titration, and the pH point of zero charge (pzc) was determined for both oxides. Crystalline structures were investigated by X-ray powder diffraction, which showed that both oxides were of the cubic system (Fm3m) with a slightly differing unit cell size. The pzc was determined for the oxides at two ionic strengths: 0.01 and 0.1 M (NaClO4). The pzc of UO2 was found to be pH 55.5 at both ionic strengths, which was supported by measurement of the isoelectric point. The corresponding result for ThO2 was approximately pH 8, seemingly varying slightly with the ionic strength. The UO2 surface was sensitive to further oxidation, which affects titration experiments by yielding ostensibly high pzc unless the oxidation is prevented. Inert, or at least O2 and CO2 free, conditions are thus necessary during work with UO2.
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6.
  • Hollfelder, Nina, 1985- (creator_code:aut_t)
  • Population genetic history and patterns of admixture : Examples from northeastern and southern Africa
  • 2018
  • swepub:Mat_doctoralthesis_t (swepub:level_scientificother_t)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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7.
  • Mattila, Tiina M., et al. (creator_code:aut_t)
  • Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe
  • 2023
  • record:In_t: Communications Biology. - : Springer Nature. - 2399-3642. ; 6:1
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show similar patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic, and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4000 years, from the Mesolithic to the end of the Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River. Genome-wide sequencing of 56 ancient hunter-gatherer and early farmer individuals from Stone Age Central and Eastern Europe reveals striking population continuity in the east in contrast to central Europe that displays extensive admixture.
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8.
  • Ausmees, Kristiina, et al. (creator_code:aut_t)
  • An empirical evaluation of genotype imputation of ancient DNA
  • 2022
  • record:In_t: G3. - : Oxford University Press. - 2160-1836. ; 12:6
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • With capabilities of sequencing ancient DNA to high coverage often limited by sample quality or cost, imputation of missing genotypes presents a possibility to increase the power of inference as well as cost-effectiveness for the analysis of ancient data. However, the high degree of uncertainty often associated with ancient DNA poses several methodological challenges, and performance of imputation methods in this context has not been fully explored. To gain further insights, we performed a systematic evaluation of imputation of ancient data using Beagle v4.0 and reference data from phase 3 of the 1000 Genomes project, investigating the effects of coverage, phased reference, and study sample size. Making use of five ancient individuals with high-coverage data available, we evaluated imputed data for accuracy, reference bias, and genetic affinities as captured by principal component analysis. We obtained genotype concordance levels of over 99% for data with 1× coverage, and similar levels of accuracy and reference bias at levels as low as 0.75×. Our findings suggest that using imputed data can be a realistic option for various population genetic analyses even for data in coverage ranges below 1×. We also show that a large and varied phased reference panel as well as the inclusion of low- to moderate-coverage ancient individuals in the study sample can increase imputation performance, particularly for rare alleles. In-depth analysis of imputed data with respect to genetic variants and allele frequencies gave further insight into the nature of errors arising during imputation, and can provide practical guidelines for postprocessing and validation prior to downstream analysis.
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9.
  • Ausmees, Kristiina (creator_code:aut_t)
  • Efficient computational methods for applications in genomics
  • 2019
  • swepub:Mat_licentiatethesis_t (swepub:level_scientificother_t)abstract
    • During the last two decades, advances in molecular technology have facilitated the sequencing and analysis of ancient DNA recovered from archaeological finds, contributing to novel insights into human evolutionary history. As more ancient genetic information has become available, the need for specialized methods of analysis has also increased. In this thesis, we investigate statistical and computational models for analysis of genetic data, with a particular focus on the context of ancient DNA.The main focus is on 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 discuss preliminary results from a simulation study comparing two methods of phasing and imputation, which suggest that the parametric Li and Stephens framework may be more robust to extremely low levels of sparsity than the parsimonious Browning and Browning model.An evaluation of methods to handle missing data in the application of PCA for dimensionality reduction of genotype data is also presented. We illustrate that non-overlapping sequence data can lead to artifacts in projected scores, and evaluate different methods for handling unobserved genotypes.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 last part of this thesis addresses the use of cloud resources for facilitating such analysis. We present two different cloud-based solutions, and exemplify them on applications from genomics.
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10.
  • Breton, Gwenna, et al. (creator_code:aut_t)
  • Comparison of sequencing data processing pipelines and application to underrepresented African human populations
  • 2021
  • record:In_t: BMC Bioinformatics. - : BioMed Central (BMC). - 1471-2105. ; 22:1
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Background Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools and the available genomes are increasing in number. Studies have evaluated and compared some of these technologies and tools, such as the Genome Analysis Toolkit (GATK) and its "Best Practices" bioinformatic pipelines. However, studies often focus on a few genomes of Eurasian origin in order to detect technical issues. We instead surveyed the use of the GATK tools and established a pipeline for processing high coverage full genomes from a diverse set of populations, including Sub-Saharan African groups, in order to reveal challenges from human diversity and stratification. Results We surveyed 29 studies using high-throughput sequencing data, and compared their strategies for data pre-processing and variant calling. We found that processing of data is very variable across studies and that the GATK "Best Practices" are seldom followed strictly. We then compared three versions of a GATK pipeline, differing in the inclusion of an indel realignment step and with a modification of the base quality score recalibration step. We applied the pipelines on a diverse set of 28 individuals. We compared the pipelines in terms of count of called variants and overlap of the callsets. We found that the pipelines resulted in similar callsets, in particular after callset filtering. We also ran one of the pipelines on a larger dataset of 179 individuals. We noted that including more individuals at the joint genotyping step resulted in different counts of variants. At the individual level, we observed that the average genome coverage was correlated to the number of variants called. Conclusions We conclude that applying the GATK "Best Practices" pipeline, including their recommended reference datasets, to underrepresented populations does not lead to a decrease in the number of called variants compared to alternative pipelines. We recommend to aim for coverage of > 30X if identifying most variants is important, and to work with large sample sizes at the variant calling stage, also for underrepresented individuals and populations.
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