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Biological and Environmental Research, Grant/Award Number: DEAC02-05CH11231; National Science Foundation, Grant/Award Number: HDR1934790 and BoCP-2225076; Norges Forskningsrad, Grant/Award Number: 287784; Watershed Function Scientific Focus Area and the ExaShed Project; Swiss National Science Foundation, Grant/Award Number: 182124

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Bootstrapping outperforms community-weighted approaches for estimating the shapes of phenotypic distributions

Publicated to:Methods in Ecology and Evolution. 14 (10): 2592-2610 - 2023-09-07 14(10), DOI: 10.1111/2041-210X.14160

Authors: Maitner, B.S.; Halbritter, A.H.; Telford, R.J.; Strydom, T.; Chacon, J.; Lamanna, C.; Sloat, L.L.; Kerkhoff, A.J.; Messier, J.; Rasmussen, N.; Pomati, F.; Merz, E.; Vandvik, V.; Enquist, B.J.

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Abstract

1. Estimating phenotypic distributions of populations and communities is central to many questions in ecology and evolution. These distributions can be characterized by their moments (mean, variance, skewness and kurtosis) or diversity metrics (e.g. functional richness). Typically, such moments and metrics are calculated using community-weighted approaches (e.g. abundance-weighted mean). We propose an alternative bootstrapping approach that allows flexibility in trait sampling and explicit incorporation of intraspecific variation, and show that this approach significantly improves estimation while allowing us to quantify uncertainty.2. We assess the performance of different approaches for estimating the moments of trait distributions across various sampling scenarios, taxa and datasets by comparing estimates derived from simulated samples with the true values calculated from full datasets. Simulations differ in sampling intensity (individuals per species), sampling biases (abundance, size), trait data source (local vs. global) and estimation method (two types of community-weighting, two types of bootstrapping).3. We introduce the TRAITSTRAP R package, which contains a modular and extensible set of bootstrapping and weighted-averaging functions that use community composition and trait data to estimate the moments of community trait distributions with their uncertainty. Importantly, the first function in the workflow, trait_fill, allows the user to specify hierarchical structures (e.g. plot within site, experiment vs. control, species within genus) to assign trait values to each taxon in each community sample.4. Across all taxa, simulations and metrics, bootstrapping approaches were more accurate and less biased than community-weighted approaches. With bootstrapping, a sample size of 9 or more measurements per species per trait generally included the true mean within the 95% CI. It reduced average percent errors by 26%-74% relative to community-weighting. Random sampling across all species outperformed both size-and abundance-biased sampling.5. Our results suggest randomly sampling similar to 9 individuals per sampling unit and species, covering all species in the community and analysing the data using nonparametric bootstrapping generally enable reliable inference on trait distributions, including the central moments, of communities. By providing better estimates of community trait distributions, bootstrapping approaches can improve our ability to link traits to both the processes that generate them and their effects on ecosystems.

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