| 1. |
- Säll, T., et al.
(författare)
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Chloroplast DNA indicates a single origin of the allotetraploid Arabidopsis suecica
- 2003
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Ingår i: Journal of Evolutionary Biology. - : John Wiley & Sons Inc.. - 1010-061X .- 1420-9101. ; 16:5, s. 1019-1029
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Tidskriftsartikel (refereegranskat)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
(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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| 3. |
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| 4. |
- Nyström, Veronica, et al.
(författare)
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Microsatellite genotyping reveals end-Pleistocene decline in mammoth autosomal genetic variation
- 2012
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 21:14, s. 3391-3402
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Tidskriftsartikel (refereegranskat)abstract
- The last glaciation was a dynamic period with strong impact on the demography of many species and populations. In recent years, mitochondrial DNA sequences retrieved from radiocarbon-dated remains have provided novel insights into the history of Late Pleistocene populations. However, genotyping of loci from the nuclear genome may provide enhanced resolution of population-level changes. Here, we use four autosomal microsatellite DNA markers to investigate the demographic history of woolly mammoths (Mammuthus primigenius) in north-eastern Siberia from before 60 000 years ago up until the species final disappearance c. 4000 years ago. We identified two genetic groups, implying a marked temporal genetic differentiation between samples with radiocarbon ages older than 12 thousand radiocarbon years before present (ka) and those younger than 9 ka. Simulation-based analysis indicates that this dramatic change in genetic composition, which included a decrease in individual heterozygosity of approximately 30%, was due to a multifold reduction in effective population size. A corresponding reduction in genetic variation was also detected in the mitochondrial DNA, where about 65% of the diversity was lost. We observed no further loss in genetic variation during the Holocene, which suggests a rapid final extinction event.
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| 5. |
- Omrak, Ayça, et al.
(författare)
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Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool
- 2016
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 26:2, s. 270-275
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Tidskriftsartikel (refereegranskat)abstract
- Anatolia and the Near East have long been recognized as the epicenter of the Neolithic expansion through archaeological evidence. Recent archaeogenetic studies on Neolithic European human remains have shown that the Neolithic expansion in Europe was driven westward and northward by migration from a supposed Near Eastern origin [1-5]. However, this expansion and the establishment of numerous culture complexes in the Aegean and Balkans did not occur until 8,500 before present (BP), over 2,000 years after the initial settlements in the Neolithic core area [6-9]. We present ancient genome-wide sequence data from 6,700-year-old human remains excavated from a Neolithic context in Kumtepe, located in northwestern Anatolia near the well-known (and younger) site Troy [10]. Kumtepe is one of the settlements that emerged around 7,000 BP, after the initial expansion wave brought Neolithic practices to Europe. We show that this individual displays genetic similarities to the early European Neolithic gene pool and modern-day Sardinians, as well as a genetic affinity to modern-day populations from the Near East and the Caucasus. Furthermore, modern-day Anatolians carry signatures of several admixture events from different populations that have diluted this early Neolithic farmer component, explaining why modern-day Sardinian populations, instead of modern-day Anatolian populations, are genetically more similar to the people that drove the Neolithic expansion into Europe. Anatolia's central geographic location appears to have served as a connecting point, allowing a complex contact network with other areas of the Near East and Europe throughout, and after, the Neolithic.
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| 6. |
- Olsson, Mattias, 1975, et al.
(författare)
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Sorption of Pu(III-IV) onto TiO2: A Preliminary Study
- 2003
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Ingår i: Materials Research Society Symposium Proceedings. - 155899694X ; 757, s. 517-522
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Konferensbidrag (refereegranskat)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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| 7. |
- Olsson, Mattias, 1975, et al.
(författare)
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Sorption of Pu(VI) onto TiO2
- 2003
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Ingår i: Journal of Colloid and Interface Science. ; 266:2, s. 269-275
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Tidskriftsartikel (refereegranskat)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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| 8. |
- Olsson, Mattias, 1975, et al.
(författare)
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Surface Charge Densities of Two Actinide(IV) Oxides: UO2 and ThO2
- 2002
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Ingår i: Journal of Colloid and Interface Science. - 1095-7103 .- 0021-9797. ; 256:2, s. 256-261
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Tidskriftsartikel (refereegranskat)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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| 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. |
- Kirdok, Emrah, et al.
(författare)
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Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals
- 2024
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.
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