TY - JOUR
T1 - Bootstrapping outperforms community-weighted approaches for estimating the shapes of phenotypic distributions
AU - Maitner, Brian S.
AU - Halbritter, Aud H.
AU - Telford, Richard J.
AU - Strydom, Tanya
AU - Chacon, Julia
AU - Lamanna, Christine
AU - Sloat, Lindsey L.
AU - Kerkhoff, Andrew J.
AU - Messier, Julie
AU - Rasmussen, Nick
AU - Pomati, Francesco
AU - Merz, Ewa
AU - Vandvik, Vigdis
AU - Enquist, Brian J.
N1 - Publisher Copyright:
© 2023 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society.
PY - 2023/10
Y1 - 2023/10
N2 - 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. 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). 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. 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. Our results suggest randomly sampling ~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.
AB - 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. 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). 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. 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. Our results suggest randomly sampling ~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.
KW - R package
KW - body size
KW - community ecology
KW - community-weighted mean
KW - functional ecology
KW - functional traits
KW - nonparametric bootstrapping
KW - population biology
KW - traitstrap
UR - http://www.scopus.com/inward/record.url?scp=85170530899&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85170530899&partnerID=8YFLogxK
U2 - 10.1111/2041-210X.14160
DO - 10.1111/2041-210X.14160
M3 - Article
AN - SCOPUS:85170530899
SN - 2041-210X
VL - 14
SP - 2592
EP - 2610
JO - Methods in Ecology and Evolution
JF - Methods in Ecology and Evolution
IS - 10
ER -