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Sökning: WFRF:(Jakobsson Mattias) > Tidskriftsartikel

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1.
  • Säll, T., et al. (författare)
  • Chloroplast DNA indicates a single origin of the allotetraploid Arabidopsis suecica
  • 2003
  • Ingår i: Journal of Evolutionary Biology. - : John Wiley & Sons Inc.. - 1010-061X .- 1420-9101. ; 16:5, s. 1019-1029
  • 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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3.
  • Anava, Sarit, et al. (författare)
  • Illuminating Genetic Mysteries of the Dead Sea Scrolls
  • 2020
  • Ingår i: Cell. - : CELL PRESS. - 0092-8674 .- 1097-4172. ; 181:6, s. 1218-
  • Tidskriftsartikel (refereegranskat)abstract
    • The discovery of the 2,000-year-old Dead Sea Scrolls had an incomparable impact on the historical understanding of Judaism and Christianity. "Piecing together'' scroll fragments is like solving jigsaw puzzles with an unknown number of missing parts. We used the fact that most scrolls are made from animal skins to "fingerprint'' pieces based on DNA sequences. Genetic sorting of the scrolls illuminates their textual relationship and historical significance. Disambiguating the contested relationship between Jeremiah fragments supplies evidence that some scrolls were brought to the Qumran caves from elsewhere; significantly, they demonstrate that divergent versions of Jeremiah circulated in parallel throughout Israel (ancient Judea). Similarly, patterns discovered in non-biblical scrolls, particularly the Songs of the Sabbath Sacrifice, suggest that the Qumran scrolls represent the broader cultural milieu of the period. Finally, genetic analysis divorces debated fragments from the Qumran scrolls. Our study demonstrates that interdisciplinary approaches enrich the scholar's toolkit.
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4.
  • Andersson, Mattias, et al. (författare)
  • Intrinsic and extrinsic influences on the temperature dependence of mobility in conjugated polymers
  • 2008
  • Ingår i: Organic electronics. - : Elsevier. - 1566-1199 .- 1878-5530. ; 9:5, s. 569-574
  • Tidskriftsartikel (refereegranskat)abstract
    • The temperature dependence of charge carrier mobility in conjugated polymers and their blends with fullerenes is investigated with different electrical methods, through field effect transistor (FET), space charge limited current (SCLC) and charge extraction (CELIV) measurements. Simple models, such as the Gaussian disorder model (GDM), are shown to accurately predict the temperature behavior, and a good correlation between the different measurement methods is obtained. Inconsistent charge carrier concentrations in the modeling are explained through intrinsic non-equilibrium effects, and are responsible for the limited applicability of existing numerical models. A severe extrinsic influence from water in FETs with a hydrophilic insulator interface is also demonstrated. The presence of water leads to a significant overestimate of the disorder in the materials from measurements close to room temperature and erratic behavior in the 150-350 K range. To circumvent this problem it is shown to be necessary to measure under ultra high vacuum (UHV) conditions. © 2008 Elsevier B.V. All rights reserved.
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5.
  • Ausmees, Kristiina, et al. (författare)
  • An empirical evaluation of genotype imputation of ancient DNA
  • 2022
  • Ingår i: G3. - : Oxford University Press. - 2160-1836. ; 12:6
  • Tidskriftsartikel (refereegranskat)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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6.
  • Babiker, Hiba, et al. (författare)
  • Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci.
  • 2011
  • Ingår i: Investigative Genetics. - : Springer Science and Business Media LLC. - 2041-2223. ; 2:1
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region.RESULT: We report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE) was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia.CONCLUSION: We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.
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7.
  • Blank, Malou, 1975, et al. (författare)
  • Mobility patterns in inland southwestern Sweden during the Neolithic and Early Bronze Age
  • 2021
  • Ingår i: Archaeological and Anthropological Sciences. - : Springer Science and Business Media LLC. - 1866-9557 .- 1866-9565. ; 13
  • Tidskriftsartikel (refereegranskat)abstract
    • In this paper, we investigate population dynamics in the Scandinavian Neolithic and Early Bronze Age in southwestern Sweden. Human mobility patterns in Falbygden were studied by applying strontium isotope analysis combined with archaeological and bioarchaeological data, including mtDNA and sex assessment on a large dataset encompassing 141 individuals from 21 megalithic graves. In combination with other archaeological and anthropological records, we investigated the temporal and spatial scale of individual movement, mobility patterns of specific categories of people and possible social drivers behind them. Our results of strontium and biomolecular analyses suggest that mobility increased in the Late Neolithic and Early Bronze Age compared to the earlier parts of the Neolithic. The data indicate individuals moving both into and away from Falbygden. Mobility patterns and contact networks also shift over time.
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8.
  • Blum, Michael G. B., et al. (författare)
  • Deep Divergences of Human Gene Trees and Models of Human Origins
  • 2011
  • Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 28:2, s. 889-898
  • Tidskriftsartikel (refereegranskat)abstract
    • Two competing hypotheses are at the forefront of the debate on modern human origins. In the first scenario, known as the recent Out-of-Africa hypothesis, modern humans arose in Africa about 100,000-200,000 years ago and spread throughout the world by replacing the local archaic human populations. By contrast, the second hypothesis posits substantial gene flow between archaic and emerging modern humans. In the last two decades, the young time estimates-between 100,000 and 200,000 years-of the most recent common ancestors for the mitochondrion and the Y chromosome provided evidence in favor of a recent African origin of modern humans. However, the presence of very old lineages for autosonnal and X-linked genes has often been claimed to be incompatible with a simple, single origin of modern humans. Through the analysis of a public DNA sequence database, we find, similar to previous estimates, that the common ancestors of autosomal and X-linked genes are indeed very old, living, on average, respectively, 1,500,000 and 1,000,000 years ago. However, contrary to previous conclusions, we find that these deep gene genealogies are consistent with the Out-of-Africa scenario provided that the ancestral effective population size was approximately 14,000 individuals. We show that an ancient bottleneck in the Middle Pleistocene, possibly arising from an ancestral structured population, can reconcile the contradictory findings from the mitochondrion on the one hand, with the autosomes and the X chromosome on the other hand.
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9.
  • Bradshaw, Clare, et al. (författare)
  • Physical Disturbance by Bottom Trawling Suspends Particulate Matter and Alters Biogeochemical Processes on and Near the Seafloor
  • 2021
  • Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 8
  • Tidskriftsartikel (refereegranskat)abstract
    • Bottom trawling is known to affect benthic faunal communities but its effects on sediment suspension and seabed biogeochemistry are less well described. In addition, few studies have been carried out in the Baltic Sea, despite decades of trawling in this unique brackish environment and the frequent occurrence of trawling in areas where hypoxia and low and variable salinity already act as ecosystem stressors. We measured the physical and biogeochemical impacts of an otter trawl on a muddy Baltic seabed. Multibeam bathymetry revealed a 36 m-wide trawl track, comprising parallel furrows and sediment piles caused by the trawl doors and shallower grooves from the groundgear, that displaced 1,000 m3 (500 t) sediment and suspended 9.5 t sediment per km of track. The trawl doors had less effect than the rest of the gear in terms of total sediment mass but per m2 the doors had 5× the displacement and 2× the suspension effect, due to their greater penetration and hydrodynamic drag. The suspended sediment spread >1 km away over the following 3–4 days, creating a 5–10 m thick layer of turbid bottom water. Turbidity reached 4.3 NTU (7 mgDW L–1), 550 m from the track, 20 h post-trawling. Particulate Al, Ti, Fe, P, and Mn were correlated with the spatio-temporal pattern of suspension. There was a pulse of dissolved N, P, and Mn to a height of 10 m above the seabed within a few hundred meters of the track, 2 h post-trawling. Dissolved methane concentrations were elevated in the water for at least 20 h. Sediment biogeochemistry in the door track was still perturbed after 48 h, with a decreased oxygen penetration depth and nutrient and oxygen fluxes across the sediment-water interface. These results clearly show the physical effects of bottom trawling, both on seabed topography (on the scale of km and years) and on sediment and particle suspension (on the scale of km and days-weeks). Alterations to biogeochemical processes suggest that, where bottom trawling is frequent, sediment biogeochemistry may not have time to recover between disturbance events and elevated turbidity may persist, even outside the trawled area.
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10.
  • Breton, Gwenna, et al. (författare)
  • Comparison of sequencing data processing pipelines and application to underrepresented African human populations
  • 2021
  • Ingår i: BMC Bioinformatics. - : BioMed Central (BMC). - 1471-2105. ; 22:1
  • Tidskriftsartikel (refereegranskat)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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