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  • 1
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    Online Resource
    Maintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population
    Oxford University Press (OUP) ; 2021
    In:  Molecular Biology and Evolution Vol. 38, No. 5 ( 2021-05-04), p. 1820-1836
    Details
    In: Molecular Biology and Evolution, Oxford University Press (OUP), Vol. 38, No. 5 ( 2021-05-04), p. 1820-1836
    Abstract: During range expansion, edge populations are expected to face increased genetic drift, which in turn can alter and potentially compromise adaptive dynamics, preventing the removal of deleterious mutations and slowing down adaptation. Here, we contrast populations of the European subspecies Arabidopsis lyrata ssp. petraea, which expanded its Northern range after the last glaciation. We document a sharp decline in effective population size in the range-edge population and observe that nonsynonymous variants segregate at higher frequencies. We detect a 4.9% excess of derived nonsynonymous variants per individual in the range-edge population, suggesting an increase of the genomic burden of deleterious mutations. Inference of the fitness effects of mutations and modeling of allele frequencies under the explicit demographic history of each population predicts a depletion of rare deleterious variants in the range-edge population, but an enrichment for fixed ones, consistent with the bottleneck effect. However, the demographic history of the range-edge population predicts a small net decrease in per-individual fitness. Consistent with this prediction, the range-edge population is not impaired in its growth and survival measured in a common garden experiment. We further observe that the allelic diversity at the self-incompatibility locus, which ensures strict outcrossing and evolves under negative frequency-dependent selection, has remained unchanged. Genomic footprints indicative of selective sweeps are broader in the Northern population but not less frequent. We conclude that the outcrossing species A. lyrata ssp. petraea shows a strong resilience to the effect of range expansion.
    Type of Medium: Online Resource
    ISSN: 1537-1719
    URL: Article
    DOI: 10.1093/molbev/msaa322
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2024221-9
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  • 2
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    Genomic Patterns of Local Adaptation under Gene Flow in Arabidopsis lyrata
    Oxford University Press (OUP) ; 2019
    In:  Molecular Biology and Evolution Vol. 36, No. 11 ( 2019-11-01), p. 2557-2571
    Details
    In: Molecular Biology and Evolution, Oxford University Press (OUP), Vol. 36, No. 11 ( 2019-11-01), p. 2557-2571
    Abstract: Short-scale local adaptation is a complex process involving selection, migration, and drift. The expected effects on the genome are well grounded in theory but examining these on an empirical level has proven difficult, as it requires information about local selection, demographic history, and recombination rate variation. Here, we use locally adapted and phenotypically differentiated Arabidopsis lyrata populations from two altitudinal gradients in Norway to test these expectations at the whole-genome level. Demography modeling indicates that populations within the gradients diverged 〈 2 kya and that the sites are connected by gene flow. The gene flow estimates are, however, highly asymmetric with migration from high to low altitudes being several times more frequent than vice versa. To detect signatures of selection for local adaptation, we estimate patterns of lineage-specific differentiation among these populations. Theory predicts that gene flow leads to concentration of adaptive loci in areas of low recombination; a pattern we observe in both lowland-alpine comparisons. Although most selected loci display patterns of conditional neutrality, we found indications of genetic trade-offs, with one locus particularly showing high differentiation and signs of selection in both populations. Our results further suggest that resistance to solar radiation is an important adaptation to alpine environments, while vegetative growth and bacterial defense are indicated as selected traits in the lowland habitats. These results provide insights into genetic architectures and evolutionary processes driving local adaptation under gene flow. We also contribute to understanding of traits and biological processes underlying alpine adaptation in northern latitudes.
    Type of Medium: Online Resource
    ISSN: 0737-4038 , 1537-1719
    URL: Article
    DOI: 10.1093/molbev/msz149
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2024221-9
    SSG: 12
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  • 3
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    Marker-controlled watershed with deep edge emphasis and optimized H-minima transform for automatic segmentation of densely cultivated 3D cell nuclei
    Springer Science and Business Media LLC ; 2022
    In:  BMC Bioinformatics Vol. 23, No. 1 ( 2022-07-21)
    Details
    In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 23, No. 1 ( 2022-07-21)
    Abstract: The segmentation of 3D cell nuclei is essential in many tasks, such as targeted molecular radiotherapies (MRT) for metastatic tumours, toxicity screening, and the observation of proliferating cells. In recent years, one popular method for automatic segmentation of nuclei has been deep learning enhanced marker-controlled watershed transform. In this method, convolutional neural networks (CNNs) have been used to create nuclei masks and markers, and the watershed algorithm for the instance segmentation. We studied whether this method could be improved for the segmentation of densely cultivated 3D nuclei via developing multiple system configurations in which we studied the effect of edge emphasizing CNNs, and optimized H-minima transform for mask and marker generation, respectively. Results The dataset used for training and evaluation consisted of twelve in vitro cultivated densely packed 3D human carcinoma cell spheroids imaged using a confocal microscope. With this dataset, the evaluation was performed using a cross-validation scheme. In addition, four independent datasets were used for evaluation. The datasets were resampled near isotropic for our experiments. The baseline deep learning enhanced marker-controlled watershed obtained an average of 0.69 Panoptic Quality (PQ) and 0.66 Aggregated Jaccard Index (AJI) over the twelve spheroids. Using a system configuration, which was otherwise the same but used 3D-based edge emphasizing CNNs and optimized H-minima transform, the scores increased to 0.76 and 0.77, respectively. When using the independent datasets for evaluation, the best performing system configuration was shown to outperform or equal the baseline and a set of well-known cell segmentation approaches. Conclusions The use of edge emphasizing U-Nets and optimized H-minima transform can improve the marker-controlled watershed transform for segmentation of densely cultivated 3D cell nuclei. A novel dataset of twelve spheroids was introduced to the public.
    Type of Medium: Online Resource
    ISSN: 1471-2105
    URL: Article
    DOI: 10.1186/s12859-022-04827-3
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2041484-5
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  • 4
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    A ring-like accretion structure in M87 connecting its black hole and jet
    Springer Science and Business Media LLC ; 2023
    In:  Nature Vol. 616, No. 7958 ( 2023-04-27), p. 686-690
    Details
    In: Nature, Springer Science and Business Media LLC, Vol. 616, No. 7958 ( 2023-04-27), p. 686-690
    Abstract: The nearby radio galaxy M87 is a prime target for studying black hole accretion and jet formation 1,2 . Event Horizon Telescope observations of M87 in 2017, at a wavelength of 1.3 mm, revealed a ring-like structure, which was interpreted as gravitationally lensed emission around a central black hole 3 . Here we report images of M87 obtained in 2018, at a wavelength of 3.5 mm, showing that the compact radio core is spatially resolved. High-resolution imaging shows a ring-like structure of $${8.4}_{-1.1}^{+0.5}$$ 8.4 − 1.1 + 0.5 Schwarzschild radii in diameter, approximately 50% larger than that seen at 1.3 mm. The outer edge at 3.5 mm is also larger than that at 1.3 mm. This larger and thicker ring indicates a substantial contribution from the accretion flow with absorption effects, in addition to the gravitationally lensed ring-like emission. The images show that the edge-brightened jet connects to the accretion flow of the black hole. Close to the black hole, the emission profile of the jet-launching region is wider than the expected profile of a black-hole-driven jet, suggesting the possible presence of a wind associated with the accretion flow.
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
    URL: Article
    DOI: 10.1038/s41586-023-05843-w
    RVK:
    TA 1000
    RVK:
    UA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 120714-3
    detail.hit.zdb_id: 1413423-8
    SSG: 11
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  • 5
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    Local adaptation and ecological differentiation under selection, migration, and drift in Arabidopsis lyrata * : LOCAL ADAPTATION UNDER GENE FLOW AND DRIFT
    Wiley ; 2018
    In:  Evolution Vol. 72, No. 7 ( 2018-07), p. 1373-1386
    Details
    In: Evolution, Wiley, Vol. 72, No. 7 ( 2018-07), p. 1373-1386
    Type of Medium: Online Resource
    ISSN: 0014-3820
    URL: Issue
    URL: Article
    DOI: 10.1111/evo.2018.72.issue-7
    DOI: 10.1111/evo.13502
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2036375-8
    SSG: 12
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  • 6
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    Role of vernalization and of duplicated FLOWERING LOCUS C in the perennial Arabidopsis lyrata
    Wiley ; 2013
    In:  New Phytologist Vol. 197, No. 1 ( 2013-01), p. 323-335
    Details
    In: New Phytologist, Wiley, Vol. 197, No. 1 ( 2013-01), p. 323-335
    Abstract: FLOWERING LOCUS C ( FLC ) is one of the main genes influencing the vernalization requirement and natural flowering time variation in the annual A rabidopsis thaliana . Here we studied the effects of vernalization on flowering and its genetic basis in the perennial A rabidopsis lyrata . Two tandemly duplicated FLC genes ( FLC 1 and FLC 2 ) were compared with respect to expression and DNA sequence. The effect of vernalization on flowering and on the expression of FLC 1 was studied in three European populations. The genetic basis of the FLC 1 expression difference between two of the populations was further studied by expression quantitative trait locus ( eQTL ) mapping and sequence analysis. FLC 1 was shown to have a likely role in the vernalization requirement for flowering in A. lyrata . Vernalization decreased its expression and the northern study populations showed higher FLC 1 expression than the southern one. eQTL mapping between two of the populations revealed one eQTL affecting FLC1 expression in the genomic region containing the FLC genes. Most FLC 1 sequence differences between the study populations were found in the promoter region and in the first intron. Variation in the FLC 1 sequence may cause differences in FLC 1 expression between late‐ and early‐flowering A. lyrata populations.
    Type of Medium: Online Resource
    ISSN: 0028-646X , 1469-8137
    URL: Issue
    URL: Article
    DOI: 10.1111/nph.2012.197.issue-1
    DOI: 10.1111/j.1469-8137.2012.04378.x
    Language: English
    Publisher: Wiley
    Publication Date: 2013
    detail.hit.zdb_id: 208885-X
    detail.hit.zdb_id: 1472194-6
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  • 7
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    Role of seed germination in adaptation and reproductive isolation in Arabidopsis lyrata
    Wiley ; 2017
    In:  Molecular Ecology Vol. 26, No. 13 ( 2017-07), p. 3484-3496
    Details
    In: Molecular Ecology, Wiley, Vol. 26, No. 13 ( 2017-07), p. 3484-3496
    Abstract: Seed germination is an important developmental and life history stage. Yet, the evolutionary impact of germination has mainly been studied in the context of dormancy, or for its role in reproductive isolation between species. Here, we aim to examine multiple consequences of genetic divergence on germination traits between two Arabidopsis lyrata subspecies: ssp. petraea (Eurasia) and ssp. lyrata (North America). Postdormancy germination time, a potentially adaptive trait, showed differentiation between the populations, and quantitative trait loci ( QTL ) mapping revealed that the trait variation is mainly controlled by two antagonistic loci. These QTL areas contain several candidate genes with known function in postdormancy germination in A. thaliana . The sequence variation of three genes was consistent with differential selection, and they also included fixed nonsynonymous substitutions with potential to account for the phenotypic differentiation. We further show that the divergence between the subspecies has led to a slight but significant reduction in hybrid germination proportions, indicating incipient reproductive isolation. Comparison of reciprocal F 1 and F 2 progenies suggests that Bateson–Dobzhansky–Muller incompatibilities likely act through uniparentally inherited factors. Examination of genomewide transmission ratio distortion further revealed that cytonuclear interactions cause substantial pregermination inviability in the hybrids. These results confirm that seed germination has adaptive potential beyond the dormancy stage and that hybrid seed inviability can be one of the first reproductive barriers to arise during divergence.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.2017.26.issue-13
    DOI: 10.1111/mec.14135
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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  • 8
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    A recent local sweep at the PHYA locus in the N orthern E uropean S piterstulen population of Arabidopsis lyrata
    Wiley ; 2014
    In:  Molecular Ecology Vol. 23, No. 5 ( 2014-03), p. 1040-1052
    Details
    In: Molecular Ecology, Wiley, Vol. 23, No. 5 ( 2014-03), p. 1040-1052
    Abstract: Northern and central E uropean Arabidopsis lyrata ssp. petraea populations are locally adapted to prevailing climatic conditions through differences in timing of life history events. The timing of flowering and, in perennials, the timing of growth cessation influence fitness. Phytochrome A may have an important role in regulating these life history traits as it perceives changes in daylength. We asked whether PHYA has contributed to local adaptation to the northern conditions in A. l. petraea . To search for signals of directional selection at the PHYA locus, we resequenced PHYA and 9 short fragments around PHYA from a 57‐kb region from a G erman ( P lech) and a N orwegian ( S piterstulen) population and compared patterns of differentiation and diversity to a set of 19 reference loci around the genome. First, we found that the populations were highly differentiated: there were three nonsynonymous fixed differences at the PHYA locus, which was in stark contrast with the total four fixed differences in the 19 reference loci. Compatible with a sweep hypothesis, variation was almost completely removed from the 9.4‐kb region around PHYA in the northern S piterstulen population. The overall level of linkage disequilibrium ( LD ) was higher in S piterstulen, but there was no LD across the PHYA locus in the population, which is also a known consequence of a selective sweep. The sweep has likely occurred after the last glacial maximum, which suggests that it has contributed to adaptation to the northern conditions.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.2014.23.issue-5
    DOI: 10.1111/mec.12682
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2014
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
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  • 9
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    Selection for population‐specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post‐glacial colonization
    Wiley ; 2016
    In:  Molecular Ecology Vol. 25, No. 2 ( 2016-01), p. 581-597
    Details
    In: Molecular Ecology, Wiley, Vol. 25, No. 2 ( 2016-01), p. 581-597
    Abstract: Spatially varying selection can lead to population‐specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location‐specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population‐specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20% of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population‐specific nature of selection and suggested that photoperiodic adaptation was important during postglacial colonization of the species.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.2016.25.issue-2
    DOI: 10.1111/mec.13489
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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  • 10
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    Navigated transcranial magnetic stimulation of the primary somatosensory cortex impairs perceptual processing of tactile temporal discrimination
    Elsevier BV ; 2008
    In:  Neuroscience Letters Vol. 437, No. 2 ( 2008-5), p. 144-147
    Details
    In: Neuroscience Letters, Elsevier BV, Vol. 437, No. 2 ( 2008-5), p. 144-147
    Type of Medium: Online Resource
    ISSN: 0304-3940
    URL: Article
    DOI: 10.1016/j.neulet.2008.03.093
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2008
    detail.hit.zdb_id: 1498535-4
    SSG: 12
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