Papers by Meredith Schuman
IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing
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Global Ecology and Biogeography, May 16, 2023
AimGlobally distributed plant trait data are increasingly used to understand relationships betwee... more AimGlobally distributed plant trait data are increasingly used to understand relationships between biodiversity and ecosystem processes. However, global trait databases are sparse because they are compiled from many, mostly small databases. This sparsity in both trait space completeness and geographical distribution limits the potential for both multivariate and global analyses. Thus, ‘gap‐filling’ approaches are often used to impute missing trait data. Recent methods, like Bayesian hierarchical probabilistic matrix factorization (BHPMF), can impute large and sparse data sets using side information. We investigate whether BHPMF imputation leads to biases in trait space and identify aspects influencing bias to provide guidance for its usage.InnovationWe use a fully observed trait data set from which entries are randomly removed, along with extensive but sparse additional data. We use BHPMF for imputation and evaluate bias by: (1) accuracy (residuals, RMSE, trait means), (2) correlations (bi‐ and multivariate) and (3) taxonomic and functional clustering (valuewise, uni‐ and multivariate). BHPMF preserves general patterns of trait distributions but induces taxonomic clustering. Data set–external trait data had little effect on induced taxonomic clustering and stabilized trait–trait correlations.Main ConclusionsOur study extends the criteria for the evaluation of gap‐filling beyond RMSE, providing insight into statistical data structure and allowing better informed use of imputed trait data, with improved practice for imputation. We expect our findings to be valuable beyond applications in plant ecology, for any study using hierarchical side information for imputation.
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Research Square (Research Square), Mar 20, 2023
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Science, Jun 19, 2020
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AGU Fall Meeting Abstracts, Dec 1, 2020
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Remote Sensing of Environment, May 1, 2023
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International journal of applied earth observation and geoinformation, Nov 1, 2022
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bioRxiv (Cold Spring Harbor Laboratory), Mar 10, 2021
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Journal of Systematics and Evolution, May 23, 2022
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Proceedings of the National Academy of Sciences of the United States of America, Jul 1, 2019
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Assisted migration programs, introducing new better adapted species at critical locations in our ... more Assisted migration programs, introducing new better adapted species at critical locations in our forests, have the potential to mitigate the adverse effects of climate change through the increase of forest diversity and resilience. While such measures entail ecological risks related with invasiveness of exotic species or outbreaks of new diseases, introducing close relatives of native species or populations from different parts of the species range is seen as the ecologically safer option. However, due to the similar appearance of closely related species, monitoring based on the external phenotype becomes difficult and leaves genetic screening as the only reliable, yet expensive option, limiting our ability to monitor large geographic areas. Reflectance spectroscopy has emerged as an important tool to assess plant functional trait distributions and taxonomic diversity, representing a rapid, scalable and integrated measure of the plant external and internal phenotype.Here, we examine the potential of leaf-level reflectance spectroscopy to discriminate between the subspecies European beech (Fagus sylvatica L.), and Oriental beech (Fagus sylvatica spp Orientalis (Lipsky) Greut. & Burd), which has been proposed as a potential candidate for assisted migration in European forests due to its greater genetic diversity and potentially higher drought tolerance. We investigated two European beech forests in France and Switzerland where Oriental beech from the Caucasus was introduced over 100 years ago next to European beech. Over the summers of 2021 and 2022, we measured leaf spectral reflectance and leaf morphological and biochemical traits from previously genotyped adult trees.Using least squares discriminant analysis (PLS-DA), we found that leaf spectral reflectance allowed the accurate discrimination of the two beech subspecies. In particular, we found that the short-wave-infrared (SWIR) region between 1450-1750 nm from top-of-canopy leaves provided the most accurate subspecies discrimination (BA = 0.86±0.08, k = 0.72±0.15). To provide a mechanistic basis of our findings, we estimated a suite of leaf traits based on spectra-derived indices and standard field and lab protocols. Phenotyping confirmed significant subspecies differences between traits that are known to govern light-plant interactions in the SWIR, including lignin, nitrogen in proteins, leaf mass per area and leaf thickness.Our study provides a basis for crown-level subspecies classifications from airborne or satellite-based imagery in the genus Fagus. Our findings provide an important starting point for the interpretation of variability in tree crown reflectance and the superior discrimination capacity we found for leaves at the top as compared to leaves at the bottom of the canopy, holds promise for the upscaling of the method using remote sensing.
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Ecosystem functioning is thought to be mediated by traits of organisms living within phylogenetic... more Ecosystem functioning is thought to be mediated by traits of organisms living within phylogenetic constraints. Plant groups of similar traits (functional groups) are likely to fit into a similar environmental niche. Characterizing functional groups’ niche space along environmental gradients would allow us to better understand patterns of trait variation.We aim at defining the global environmental niche, i.e. the trait space filled at a given environment, of different functional groups of plants. In particular, we compare the environmental functional diversity (FD) gradients of four functional plant groups. These functional groups represent major differences in size and plant economy, derived from global in situ trait data of the TRY database. We find their gradients to vary in shape and strength. For example, tall-and-slow species’ FD varies more than small-and-slow ones, with a high FD in the Mediterranean. This study's findings point to how global change may affect functional groups differently and may ultimately provide valuable insights into ecosystem functioning.
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Remote Sensing of Environment, Oct 1, 2021
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Tree Genetics & Genomes
Genetic diversity influences the evolutionary potential of forest trees under changing environmen... more Genetic diversity influences the evolutionary potential of forest trees under changing environmental conditions, thus indirectly the ecosystem services that forests provide. European beech (Fagus sylvatica L.) is a dominant European forest tree species that increasingly suffers from climate change-related die-back. Here, we conducted a systematic literature review of neutral genetic diversity in European beech and created a meta-data set of expected heterozygosity (He) from all past studies providing nuclear microsatellite data. We propose a novel approach, based on population genetic theory and a min–max scaling to make past studies comparable. Using a new microsatellite data set with unprecedented geographic coverage and various re-sampling schemes to mimic common sampling biases, we show the potential and limitations of the scaling approach. The scaled meta-dataset reveals the expected trend of decreasing genetic diversity from glacial refugia across the species range and also su...
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Remote Sensing of Environment
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<p>Values are mean±SE. (A) At higher caterpillar densities (PM Experiment), WT monocultures... more <p>Values are mean±SE. (A) At higher caterpillar densities (PM Experiment), WT monocultures tended to produce fewer flowers than other population types. (B) WT growing in the mixed culture tended to have more flowers than those growing in monocultures, while the number of flowers produced by as<i>LOX3</i> plants growing either in mono- or mixtures did not differ. (C) WT monocultures produced fewer seed capsules than as<i>LOX3</i> mono- and mixtures when caterpillar density was high. (D) At the genotype level, WT plants growing in monocultures produced fewer seed capsules than those growing in mixtures, while the number of seed capsules did not differ between as<i>LOX3</i> plants when growing in mono- or in mixtures. (E, F) When the caterpillar density was reduced and later all caterpillars were removed from the mesocosm (NI Experiment), the number of flowers did not differ between populations or genotypes. (G) as<i>LOX3</i> monocultures produced fewer seed capsules than mixed and WT monocultures. (H) At the genotype level, as<i>LOX3</i> plants growing in the monoculture had fewer seed capsules than those growing in the mixed culture while the number of seed capsules did not differ between WT plants growing in monoculture or mixed culture. Different letters indicate significant differences; n = 4; linear mixed-effects models; see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197221#pone.0197221.t004" target="_blank">Table 4</a> for complete analysis.</p
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<p>(A) The experimental mesocosm (4 x 3 x 2.5 m l x w x h) consists of 12 containers within... more <p>(A) The experimental mesocosm (4 x 3 x 2.5 m l x w x h) consists of 12 containers within a screen- and plastic-enclosed box in a glasshouse. Aluminum containers filled with soil (1, RSonline), a stainless steel 0.8 mm mesh frame (2, Scherer Insektenschutz), and a polypropylene container and plates (3 and 4, HL Kunststofftechnik) were used to build the mesocosm. <i>Nicotiana</i> substrate and other substrates are described in <b>Tables A and B in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197221#pone.0197221.s001" target="_blank">S1 File</a></b>. (B) Eight <i>N</i>. <i>attenuata</i> plants from either the same genotype (monoculture) or containing four of each genotype (mixed culture) were planted in each mesocosm container. (C) The experimental timeline shows the differences between Experiment 1 (Plant-mediated, PM) and Experiment 2 (Natural infestation, NI), including all other experimental steps (germination, transfer to the glasshouse, planting, herbivore infestation and data collection of growth and fitness parameters). Xiang Li, flower and seed capsule icons.</p
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Papers by Meredith Schuman