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  • 1
    Online Resource
    Online Resource
    Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity
    Springer Science and Business Media LLC ; 2022
    In:  Human Genetics Vol. 141, No. 1 ( 2022-01), p. 147-173
    Details
    In: Human Genetics, Springer Science and Business Media LLC, Vol. 141, No. 1 ( 2022-01), p. 147-173
    Abstract: The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management.
    Type of Medium: Online Resource
    ISSN: 0340-6717 , 1432-1203
    URL: Article
    DOI: 10.1007/s00439-021-02397-7
    RVK:
    WA 15000
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 1459188-1
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  • 2
    Online Resource
    Online Resource
    Trait variation and integration across scales: is the leaf economic spectrum present at local scales?
    Wiley ; 2017
    In:  Ecography Vol. 40, No. 6 ( 2017-06), p. 685-697
    Details
    In: Ecography, Wiley, Vol. 40, No. 6 ( 2017-06), p. 685-697
    Abstract: Trait‐based approaches have taken an increasingly dominant role in community ecology. Although trait‐based strategy dimensions such as the leaf economic spectrum (LES) have been identified primarily at global‐scales, trait variation at the community scale is often interpreted in this context. Here we argue from several lines of evidence that a research priority should be to determine whether global‐scale trait relationships hold at more local scales. We review recent literature assessing trait variation at smaller scales, and then present a case study exploring the relationship between the correlation strength of leaf traits and their similarity in variation structure across ecological scales. We find that the correlation strength between pairs of leaf traits does not predict whether the traits respond similarly to different drivers of variation. Instead, correlation strength only sets an upper bound to the dissimilarity in trait variation structure. With moderate correlation strengths, LES traits largely retain the ability to respond independently to different drivers of phenotypic variation at different scales. Recent literature and our results suggest that LES relationships may not hold at local scales. Clarifying under what conditions and at which scales the LES is consistently expressed is necessary for us to make the most of the emerging trait toolbox.
    Type of Medium: Online Resource
    ISSN: 0906-7590 , 1600-0587
    URL: Issue
    URL: Article
    DOI: 10.1111/ecog.2017.v40.i6
    DOI: 10.1111/ecog.02006
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2024917-2
    detail.hit.zdb_id: 1112659-0
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  • 3
    Online Resource
    Online Resource
    Interspecific integration of trait dimensions at local scales: the plant phenotype as an integrated network
    Wiley ; 2017
    In:  Journal of Ecology Vol. 105, No. 6 ( 2017-11), p. 1775-1790
    Details
    In: Journal of Ecology, Wiley, Vol. 105, No. 6 ( 2017-11), p. 1775-1790
    Abstract: Plant phenotypic diversity is shaped by the interplay of trade‐offs and constraints in evolution. Closely integrated groups of traits (i.e. trait dimensions) are used to classify plant phenotypic diversity into plant strategies, but we do not know the degree of interdependence among trait dimensions. To assess how selection has shaped the phenotypic space, we examine whether trait dimensions are independent. We gathered data on saplings of 24 locally coexisting tree species in a temperate forest, and examined the correlation structure of 20 leaf, branch, stem and root traits. These traits fall into three well‐established trait dimensions (the leaf economic spectrum, the wood spectrum and Corner's Rules) that characterize vital plant functions: resource acquisition, sap transport, mechanical support and canopy architecture. Using ordinations, network analyses and Mantel tests, we tested whether the sapling phenotype of these tree species is organized along independent trait dimensions. Across species, the sapling phenotype is not structured into clear trait dimensions. The trait relationships defining trait dimensions are either weak or absent and do not dominate the correlation structure of the sapling phenotype as a whole. Instead traits from the three commonly recognized trait dimensions are organized into an integrated trait network. The effect of phylogeny on trait correlations is minimal. Our results indicate that trait dimensions apparent in broad‐based interspecific surveys do not hold up among locally coexisting species. Furthermore, architectural traits appear central to the phenotypic network, suggesting a pivotal role for branching architecture in linking resource acquisition, mechanical support and hydraulic functions. Synthesis . Our study indicates that local and global patterns of phenotypic integration differ and calls into question the use of trait dimensions at local scales. We propose that a network approach to assessing plant function more effectively reflects the multiple trade‐offs and constraints shaping the phenotype in locally co‐occurring species.
    Type of Medium: Online Resource
    ISSN: 0022-0477 , 1365-2745
    URL: Issue
    URL: Article
    DOI: 10.1111/jec.2017.105.issue-6
    DOI: 10.1111/1365-2745.12755
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 3023-5
    detail.hit.zdb_id: 2004136-6
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  • 4
    Online Resource
    Online Resource
    Detecting changes in forest floor habitat after canopy disturbance
    Wiley ; 2012
    In:  Ecological Research Vol. 27, No. 2 ( 2012-03), p. 397-406
    Details
    In: Ecological Research, Wiley, Vol. 27, No. 2 ( 2012-03), p. 397-406
    Abstract: A massive ice storm hit northeastern North America in 1998, dropping more than 100 mm of freezing rain at its epicenter in southern Quebec, Canada. There has been extensive study of which trees and areas received the most damage, but the biodiversity consequences of this damage at landscape scales have not received much attention. We assessed the effectiveness of seven remotely sensed vegetation indices—Normalized Difference Vegetation Index (NDVI), Enhanced Vegetation Index, Difference Vegetation Index, Renormalized Difference Vegetation Index, Atmospherically Resistant Vegetation Index, Green Normalized Difference Vegetation Index and Visible Atmospheric Resistant Index—for modeling the coarse woody debris (CWD) influx in an old growth forest reserve at the storm's epicenter; NDVI was the best predictor of CWD influx. We categorized the geospatial CWD predictions from the NDVI‐derived model to map the spatial distribution of sun‐exposed, moist‐shaded, dry‐shaded and wet CWD microhabitats on the forest floor. Moist‐shaded, dry‐shaded and wet patches of CWD were large and well connected, but sun‐exposed patches were small and sparse. Since these microhabitats affect the distribution and abundance of saproxylic insects, wood‐rotting fungi, salamanders, birds, small burrowing mammals and plant species dependent on nurse‐logs for establishment, the CWD influx from the 1998 ice storm may have revitalized local populations of these taxa through increased habitat availability as well as increased dispersal within the reserve.
    Type of Medium: Online Resource
    ISSN: 0912-3814 , 1440-1703
    URL: Article
    DOI: 10.1007/s11284-011-0911-7
    Language: English
    Publisher: Wiley
    Publication Date: 2012
    detail.hit.zdb_id: 2023900-2
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  • 5
    Online Resource
    Online Resource
    Similarities and differences in intrapopulation trait correlations of co‐occurring tree species: consistent water‐use relationships amid widely different correlation patterns
    Wiley ; 2018
    In:  American Journal of Botany Vol. 105, No. 9 ( 2018-09), p. 1477-1490
    Details
    In: American Journal of Botany, Wiley, Vol. 105, No. 9 ( 2018-09), p. 1477-1490
    Abstract: General relationships among functional traits have been identified across species, but the forces shaping these relationships remain largely unknown. Adopting an approach from evolutionary biology, we studied similarities and differences in intrapopulation trait correlations among locally co‐occurring tree species to assess the roles of constraints, phylogeny, and the environmental niche in shaping multivariate phenotypes. We tested the hypotheses (1) that intrapopulation correlations among functional traits are largely shaped by fundamental trade‐offs or constraints and (2) that differences among species reflect adaptation to their environmental niches. Methods We compared pairwise correlations and correlation matrices of 17 key functional traits within and among temperate tree species. These traits describe three well‐established trade‐off dimensions characterizing interspecific relationships among physiological functions: resource acquisition and conservation; sap transport and mechanical support; and branch architecture. Key Results Six trait pairs are consistently correlated within populations. Of these, only one involves dimensionally independent traits: LMA ‐δ 13 C. For all other traits, intrapopulation functional trait correlations are weak, are species‐specific, and differ from interspecific correlations. Species intrapopulation correlation matrices are related to neither phylogeny nor environmental niche. Conclusions The results (1) suggest that the functional design of these species is centered on efficient water use, (2) highlight flexibility in plant functional design across species, and (3) suggest that intrapopulation, local interspecific, and global interspecific correlations are shaped by processes acting at each of these scales.
    Type of Medium: Online Resource
    ISSN: 0002-9122 , 1537-2197
    URL: Issue
    URL: Article
    DOI: 10.1002/ajb2.2018.105.issue-9
    DOI: 10.1002/ajb2.1146
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2053581-8
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    The effects of aluminum on Picea rubens :factorial experiments using sand culture
    Canadian Science Publishing ; 1995
    In:  Canadian Journal of Forest Research Vol. 25, No. 1 ( 1995-01-01), p. 8-17
    Details
    In: Canadian Journal of Forest Research, Canadian Science Publishing, Vol. 25, No. 1 ( 1995-01-01), p. 8-17
    Abstract: We used sand culture to examine the effects of aluminum (Al 3+ ) on gas exchange and growth in 1+0 Picearubens Sarg. seedlings. Growth solutions were prepared to match the elemental concentrations of the soil solutions in a declining Abiesbalsamea (L.) Mill.–P. rubens stand. In our first experiment, we used a four-way factorial design to examine the interactions between Al, pH, nutrients, and CO 2 . All plants were nitrogen deficient. Photosynthetic rate and instantaneous water-use efficiency both declined at 250 μmol•L −1 Al, as did the root/shoot ratio of the seedlings. Plant weight, however, was not significantly affected by the 10-fold increase in Al solution concentration. These results were robust across a range of experimental conditions, suggesting that other aspects of soil acidification, such as NO 3 fertilization in N deficient soils, could counteract the toxic effects of Al. In a second experiment, we examined the effects of subtoxic concentrations of Al at two levels of nutrient cation availability. Unlike in a previous study, cation fertilization affected neither gas exchange nor growth. While the decreases in root/shoot ratio and growth were expected at 250 μmol•L −1 Al, the peak in growth rates for intermediate concentrations of Al (25–100 μmol•L −1 ) was not. The latter result was interpreted in light of the positive effects that low concentrations of Al are known to have on other species.
    Type of Medium: Online Resource
    ISSN: 0045-5067 , 1208-6037
    URL: Article
    DOI: 10.1139/x95-002
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 1995
    detail.hit.zdb_id: 1473096-0
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  • 7
    Online Resource
    Online Resource
    The role of dispersal in shaping plant community composition of wetlands within an old-growth forest : Dispersal and plant community composition
    Wiley ; 2010
    In:  Journal of Ecology Vol. 98, No. 6 ( 2010-11), p. 1292-1299
    Details
    In: Journal of Ecology, Wiley, Vol. 98, No. 6 ( 2010-11), p. 1292-1299
    Type of Medium: Online Resource
    ISSN: 0022-0477
    URL: Issue
    URL: Article
    DOI: 10.1111/jec.2010.98.issue-6
    DOI: 10.1111/j.1365-2745.2010.01708.x
    Language: English
    Publisher: Wiley
    Publication Date: 2010
    detail.hit.zdb_id: 3023-5
    detail.hit.zdb_id: 2004136-6
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  • 8
    Online Resource
    Online Resource
    Functional ecology of congeneric variation in the leaf economics spectrum
    Wiley ; 2020
    In:  New Phytologist Vol. 225, No. 1 ( 2020-01), p. 196-208
    Details
    In: New Phytologist, Wiley, Vol. 225, No. 1 ( 2020-01), p. 196-208
    Abstract: Variation in resource availability can lead to phenotypic plasticity in the traits comprising the world‐wide leaf economics spectrum ( LES ), potentially impairing plant function and complicating the use of tabulated values for LES traits in ecological studies. We compared 14 Carex (Cyperaceae) species in a factorial experiment (unshaded/shaded × sufficient/insufficient P) to analyze how changes in the network of allometric scaling relationships among LES traits influenced growth under favorable and resource‐limited conditions. Changes in leaf mass per area ( LMA ) shifted the scaling relationships among LES traits expressed per unit area vs mass in ways that helped to sustain growth under resource limitation. Increases in area‐normalized photosynthetic capacity and foliar nitrogen (N) were correlated with increased growth, offsetting losses associated with mass‐normalized dark respiration and foliar N. These shifts increased the contributions to growth associated with photosynthetic N‐use efficiency and the N : P ratio. Plasticity in LMA is at the hub of the functional role of the LES as an integrated and resilient complex system that balances the relationships among area‐ and mass‐based aspects of gas exchange and foliar nutrient traits to sustain at least some degree of plant growth under differing availabilities of above‐ and below‐ground resources.
    Type of Medium: Online Resource
    ISSN: 0028-646X , 1469-8137
    URL: Issue
    URL: Article
    DOI: 10.1111/nph.v225.1
    DOI: 10.1111/nph.16109
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 208885-X
    detail.hit.zdb_id: 1472194-6
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  • 9
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    Online Resource
    Plant species diversity and composition of wetlands within an upland forest
    Wiley ; 2008
    In:  American Journal of Botany Vol. 95, No. 10 ( 2008-10), p. 1216-1224
    Details
    In: American Journal of Botany, Wiley, Vol. 95, No. 10 ( 2008-10), p. 1216-1224
    Abstract: Though often overlooked, small wetlands in an upland matrix can support diverse plant communities that increase both local and regional species richness. Here we characterize the full range of wetland vegetation within an upland forest landscape and compare the diversity and composition of different wetland plant communities. In an old‐growth forest reserve in southern Quebec, Canada, we sampled wet habitats including lakeshores, permanent and seasonal ponds, swamps, glades, and streamsides. We used clustering, indicator species analysis, and nonmetric multidimensional scaling ordination to identify and compare vegetation types. The wetlands contained 280 species of vascular plants, 45% of the reserve's flora, in only 1.1% of its area. Local diversity averaged 24 ± 0.7 species per 7 m 2 , much higher than in the surrounding upland forests. Plant communities sorted into five types, whose strongest indicator species were Osmunda regalis, Glyceria striata, O. cinnamomea, Deparia acrostichoides , and Matteuccia struthiopteris , respectively. Both local species richness and compositional variation among sites differed among the vegetation types. By combining species representative of the region's major wetlands with species from the upland forest matrix, the plant assemblages of these wetlands make disproportionately important contributions to landscape‐level diversity.
    Type of Medium: Online Resource
    ISSN: 0002-9122 , 1537-2197
    URL: Article
    DOI: 10.3732/ajb.0800098
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2008
    detail.hit.zdb_id: 2053581-8
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  • 10
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    Online Resource
    Ecological and Evolutionary Diversification Within the Genus 〈I〉Carex〈/I〉 (Cyperaceae): Consequences for Community Assembly in Subarctic Fens
    American Society of Plant Taxonomists ; 2016
    In:  Systematic Botany Vol. 41, No. 3 ( 2016-09-01), p. 558-579
    Details
    In: Systematic Botany, American Society of Plant Taxonomists, Vol. 41, No. 3 ( 2016-09-01), p. 558-579
    Type of Medium: Online Resource
    ISSN: 0363-6445 , 1548-2324
    URL: Article
    DOI: 10.1600/036364416X692514
    Language: English
    Publisher: American Society of Plant Taxonomists
    Publication Date: 2016
    detail.hit.zdb_id: 2052625-8
    SSG: 12
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