Species-specific responses to environmental heterogeneity underpin spatial variation in annual plant communities
Data files
Jul 28, 2026 version files 159.01 KB
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exper_plant_comm_composition_20-21.csv
25.28 KB
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germinant_countdata_2021.csv
12.03 KB
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germinant_countdata_2022.csv
13.33 KB
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pcwtdata_2021.csv
18.19 KB
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pcwtdata_2022.csv
18.10 KB
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plant_comm_composition_20-21.csv
8.26 KB
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RCode.R
52.81 KB
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README.md
7.46 KB
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soil_nutrient.csv
493 B
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Species_Code.csv
3.04 KB
Abstract
Spatially heterogeneous environments can promote species coexistence through differences in how species respond to their immediate environments. It remains unclear, however, how species-specific responses to heterogeneous environments contribute to variation in the mechanisms by which community composition promotes coexistence. In this study, we use a reciprocal field experiment to examine how two sources of fine-scale spatial variation: the physical sheltering and soil conditioning separately provided by coarse woody materials (CWM) influence the composition of winter annual plant communities and the germination and growth performance of three dominant species from these communities. We found that the effects of soil conditioning and physical sheltering from CWM each contributed to spatial variation in plant composition, separately. The presence or absence of CWM in the immediate vicinity of plants explained about 10% of the variation in community composition and had a significant, species-specific effect on germination and biomass for all three focal species. A larger proportion of variation (~50%) in plant assemblages was explained by the broader-scale spatial unit of experimental blocks, suggesting that broader-scale environmental factors have a greater impact on species composition in these communities than the very localised fine-scale impacts of CWM (~10%). Our study provides empirical evidence that species-specific responses to spatial heterogeneity align with spatial variation in community composition, consistent with the prerequisite necessary for the operation of spatial coexistence mechanisms. Fine-scale spatial heterogeneity contributes to spatial variation in overall species composition, though its effect is relatively smaller than that of broader-scale spatial heterogeneity. Together, our findings suggest that plant community composition is structured through the combined influence of fine-- and broader-scale spatial processes.
Dataset DOI: 10.5061/dryad.79cnp5j83
Description of the data and file structure
Project and Data Overview
Project title: Linking species performance and community composition to environmental
heterogeneity: insights into spatial coexistence in annual plant communities
Description: Data were collected from field surveys of natural plant communities and experimental manipulations to determine how spatial heterogeneity mediates annual plant coexistence in Western Australia. Sampling took place from 2020 to 2022.
Author and contributors
- Authors: Wing Man Siu, Jake Eckersley, John M Dwyer, Margie M. Mayfield, and Aubrie R.M. James
- Date created: 2025
Contact information
Name: Wing Man Siu
Affiliation: University of Melbourne
ORCID ID: https://orcid.org/0000-0002-9875-3056
Dataset Version
- Data created: 09 Aug 2025
- Version: 1.0
Data files and structure
The dataset consists of the following files:
- germinant_countdata_2021.csv
- germinant_countdata_2022.csv
- pcwtdata_2021.csv
- pcwtdata_2022.csv
- plant_comm_composition_20-21.csv
- exper_plant_comm_composition_20-21.csv
- soil_nutrient.csv
Files and variables
File: germinant_countdata_2021.csv
Description: a comma-delimited file containing germination data from the species performance experiment conducted in 2021.
Variables
- block: Experimental block number
- transect: Treatment plot ID
- initial: Initial microsite condition ("log" or "open"), where "log" = coarse woody materials in the dataset
- current_plot_type: Current microsite classification (categorical)
- physical_barrier: Presence of physical barrier (0 = no, 1 = yes)
- name: Species code
- value: Germinant count (integer)
- presence: Presence/absence of germinant (0 = absent, 1 = present)
- posicounts: If
presence=1, positive germinant counts (integer, NA if absent)
File: germinant_countdata_2022.csv
Description: a comma-delimited file containing germination data from the species performance experiment conducted in 2022.
Variables
- block: Experimental block number
- initial: Initial microsite condition ("log" or "open"), where "log" = coarse woody materials in the dataset
- current_plot_type: Current microsite classification (categorical)
- physical_barrier: Presence of physical barrier (0 = no, 1 = yes)
- name: Species code
- value: Germinant count (integer)
- presence: Presence/absence of germinant (0 = absent, 1 = present)
- posicounts: If
presence=1, positive germinant counts (integer, NA if absent)
File: pcwtdata_2021.csv
Description: a comma-delimited file containing data of log-transformed per capita biomass data from species performance experiment conducted in 2021.
Variables
- block: Experimental block number
- transect: Treatment plot ID
- initial: Initial microsite condition ("log" or "open"), where "log" = coarse woody debris (cwd) in the dataset
- current_plot_type: Current microsite classification (categorical)
- physical_barrier: Presence of a physical sheltering (0 = no, 1 = yes)
- name: Species code
- value: Per capita dry weight of biomass (numeric, in grams; NA if absent)
- log_wt: Log-transformed per dry weight of biomass (numeric; NA if absent)
File: pcwtdata_2022.csv
Description: a comma-delimited file containing data of log-transformed per capita biomass data from species performance experiment conducted in 2022.
Variables
- block: Experimental block number
- transect: Treatment plot ID
- initial: Initial microsite condition ("log" or "open"), where "log" = coarse woody materials in the dataset
- current_plot_type: Current microsite classification (categorical)
- physical_barrier: Presence of a physical sheltering (0 = no, 1 = yes)
- name: Species code
- value: Per capita dry weight of biomass (numeric, in grams; NA if absent)
- log_wt: Log-transformed per dry weight of biomass (numeric; NA if absent)
File: exper_plant_comm_composition_20-21.csv
Description: a comma-delimited file containing community composition data from the experimental plots in 2020-2021. Each row represents a plant assemblage, and the first 87 columns correspond to counts of individual plant species in that assemblage. The remaining columns provide metadata about the plot and treatment.
Variables
- Species columns (87 total): Count of each species in the assemblage (integer)
- time: Sampling time point (categories; "t0"=2020, "t1"=2021, "t2"=2022)
- block: Experimental block number
- init: Initial microsite condition ("log"= cwd or "open"), where "log" = presence of pre-conditioning effect
- treatment: Current microsite classification/ treatment type applied to the plot (categorical)
- physical: Presence of a physical sheltering effect (integer; 0 = no, 1 = yes)
File: plant_comm_composition_20-21.csv
Description: a comma-delimited file containing CWD and Open community species composition data from the experimental plots in 2020-2021. Each row represents a plant assemblage, and the first 87 columns correspond to counts of individual plant species in that assemblage. The remaining columns provide metadata about the treatment.
Variables
- Species columns (87 total): Counts of individual species in each plant assemblage
- time: Sampling time point (categories; "t0"=2020, "t1"=2021, "t2"=2022)
- block: Experimental block number
- init: Initial microsite condition ("log"= cwd or "open")
File: soil_nutrient.csv
Description: a comma-delimited file containing soil abiotic properties data collected from 2022.
Variables
- block: Experimental block number
- plot: Treatment plot ID
- init: Initial microsite condition ("log"= CWM or "open")
- N: Plant available soil nitrogen (mg/kg)
- P: Plant available soil phosphorus (mg/kg)
- K: Plant available soil potassium (mg/kg)
- C: Soil carbon concentration (%)
- pH: Soil pH
- CEC: Cation exchange capacity (meq/100g)
File: Species_Code.csv
Description: a comma-delimited file providing a lookup table for the species codes used throughout the dataset. This file should be used as a reference when interpreting species codes in the associated community composition datasets.
Variables
- Family: Taxonomic family of the species.
- Species: Scientific name of the species, consisting of the genus and species name.
- Species code: Unique species code used consistently across all data files in this dataset.
R Script
File: RCode.R
Description: This R script reproduces all statistical analyses and figures presented in the manuscript. The script is organised into clearly labelled sections that document the analytical workflow. Each section specifies the input dataset(s) used, the analyses performed, and the corresponding outputs.
The script also includes:
- a package section listing all required R packages;
- clear annotations identifying which data files are used for each analysis;
- descriptive comments explaining each analytical step, including data preparation, statistical modelling, and figure generation.
The script was developed using R version 4.3.2. All required packages are loaded at the beginning of the script and include: lme4, emmeans, pscl, glmmTMB, tidyr, DHARMa, ggplot2, AICcmodavg, ggpubr, dplyr, labdsv, vegan, and patchwork.
Code/software
R Version 4.3.2