Data from: Inferring ecological selection from multidimensional community trait distributions along environmental gradients
Data files
May 27, 2024 version files 9.03 KB
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README.md
5.15 KB
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trait_dat.csv
3.88 KB
Abstract
Understanding the drivers of community assembly is critical for predicting the future of biodiversity and ecosystem services. Ecological selection ubiquitously shapes communities by selecting for individuals with most suitable trait combinations. Detecting selection types on key traits across environmental gradients and over time has the potential to reveal underlying abiotic and biotic drivers of community dynamics. Here we present a model-based predictive framework to quantify multidimensional trait distributions of communities (community trait niches), which we use to identify ecological selection types shaping communities along environmental gradients. We apply the framework to over 3600 boreal forest understory plant communities with results indicating that directional, stabilizing, and divergent selection all modify community trait niches and that the selection type acting on individual traits may change over time. Our results provide novel and rare empirical evidence for divergent selection within a natural system. Our approach provides a framework for identifying key traits under selection and facilitates the detection of processes underlying community dynamics.
Code and data for inferring ecological selection from multidimensional community trait distributions along environmental gradients
Boreal forest understory species trait data, applied trait analysis code, and associated model outputs for reproducing the results in the manuscript “Inferring ecological selection from multidimensional community trait distributions along environmental gradients.” Trait data include species-level mean trait values for ten functional traits (plant height, specific leaf area, leaf C:N ratio, leaf dry matter content, leaf P, leaf N, leaf N:P ratio, mycorrhizal status, clonality, and dispersal mechanism) for 39 vascular plant species located found in the understory of Finnish boreal forests. Model output from a multinomial Bayesian joint species distribution model is also provided yielding predictions of species relative abundance across 3,602 vegetation survey sites sampled in 1985-1986, 1995, and 2006 in conjunction with the 8th Finnish National Forest Inventory. Code is provided to process trait data, map predicted species relative abundance to traits, and construct multivariate trait distributions along enviromental gradients (soil fertility, growing degree days, and forest overstory density).
Description of the data and file structure
Trait data
Trait data is provided in a single comma-separated text file named “trait_dat.csv”. The rows of the data file correspond to species. The columns provide species-level mean trait values for the corresponding species. Metadata for each variable is provided below.
Identifier variables
- Species: Code for species (full species names are defined below)
- AGROCAPI: Agrostis capillaris
- BETUPUB3: Betula pubescens
- CALAARUN: Calamagrostis arundinacea
- CALLVULG: Calluna vulgaris
- CAREDIGI: Carex digitata
- CAREGLOB: Carex globularis
- CONVMAJA: Convallaria majalis
- DESCCESP: Deschampsia cespitosa
- DESCFLEX: Deschampsia flexuosa
- DRYOCART: Dryopteris carthusiana
- EMPENIGR: Empetrum nigrum
- EPILANGU: Epilobium angustifolium
- EQUISYLV: Equisetum sylvaticum
- FRAGVESC: Fragaria vesca
- GYMNDRYO: Gymnocarpium dryopteris
- JUNICOM3: Juniperus communis
- LEDUPALU: Ledum palustre
- LINNBORE: Linnaea borealis
- LUZUPILO: Luzula pilosa
- LYCOANNO: Lycopodium annotinum
- MAIABIFO: Maianthemum bifolium
- MELAPRAT: Melampyrum pratense
- MELASYLV: Melampyrum sylvaticum
- MELINUTA: Melica nutans
- ORTHSECU: Orthilia secunda
- OXALACET: Oxalis acetosella
- PICEABI3: Picea abies
- PINUSYL3: Pinus sylvestris
- POPUTRE3: Populus tremula
- PTERAQUI: Pteridium aquilinum
- RUBUIDA4: Rubus idaeus
- RUBUSAXA: Rubus saxatilis
- SOLIVIRG: Solidago virgaurea
- SORBAUC3: Sorbus aucuparia
- TRIEEURO: Lysimachia europaea
- VACCMYRT: Vaccinium myrtillus
- VACCULIG: Vaccinium uliginosum
- VACCVITI: Vaccinium vitis-idaea
- VIOLRIVI: Viola riviniana
Trait variables
- Height_cm_TRY
- SLA
- Leaf_CN_ratio
- LDMC
- Leaf_P
- Leaf_N
- Leaf_NP_ratio
- Myco_colo
- Clonality
- wind
Model results
Model results include 1,000 processed posterior samples from the multinomial Bayesian joint species distribution model described in the associated manuscript. Results are stored in a single R data file named “proc_mod_rslts.rda”. Posterior samples are provided for each parameter in the model as described below. See Itter et al., 2023 for complete definition of model and implementation details.
- delta: Site-level factor used in Poisson approximation to multinomial response
- beta: Species-specific environmental responses
- gamma: Mean environmental responses among species
- V: Variance of species-level responses to environment given a mean of gamma
- sigma: Residual species standard deviation
Code for processing and applying the trait data and model results in order to reproduce the analysis in the corresponding manuscript are described under Code/Software below.
Sharing/Access information
Data and code were derived from the following sources.
- Itter, M.S., Kaarlejärvi, E., Laine, A.L., Hamberg, L., Tonteri, T. and Vanhatalo, J., 2022. Bayesian joint species distribution model selection for community-level prediction. bioRxiv, 2022.05.03.490480; doi: https://doi.org/10.1101/2022.05.03.490480.
Code/Software
One R script file (“applied_trait_selection.R”) is provided to reproduce the analysis in the corresponding manuscript. The provided R script is described below.
“applied_trait_selection.R”: R script file that loads the data file described above along with understory composition data, processes the data to generate inputs associated with the model described in the corresponding manuscript, demonstrates the implementation of the model including post-processing, and applies processed model results to reproduce all tables and figure in the corresponding manuscript.
Boreal forest understory species trait data, applied trait analysis code, and associated model outputs for reproducing the results in the manuscript "Inferring ecological selection from multidimensional community trait distributions along environmental gradients." Trait data include species-level mean trait values for ten functional traits (plant height, specific leaf area, leaf C:N ratio, leaf dry matter content, leaf P, leaf N, leaf N:P ratio, mycorrhizal status, clonality, and dispersal mechanism) for 39 vascular plant species located found in the understory of Finnish boreal forests. Model output from a multinomial Bayesian joint species distribution model is also provided yielding predictions of species relative abundance across 3,602 vegetation survey sites sampled in 1985-1986, 1995, and 2006 in conjunction with the 8th Finnish National Forest Inventory. Code is provided to process trait data, map predicted species relative abundance to traits, and construct multivariate trait distributions along enviromental gradients (soil fertility, growing degree days, and forest overstory density).