Community trait variation drives selection on species diversity through feedback with predator density
Data files
Oct 28, 2024 version files 398.23 KB
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data_all_final.txt
333.56 KB
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data_rep_final.txt
56.13 KB
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ingestion_rate.txt
2.17 KB
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max_growth_rate.txt
1.46 KB
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README.md
4.91 KB
Abstract
Identifying the processes underlying community assembly and dynamics remains a central goal in ecology. Although much research has been devoted to analyzing how environments affect species diversity, fewer studies have resolved the link between the fundamental process of ecological selection and species diversity. It has been suggested that identifying ecological selection by estimating changes in community-weighted variance (CWV) and mean (CWM) of functional traits may help to identify more general rules of community assembly. Here, we asked whether and how selection by predation and competition affect species diversity, and how this is determined by the initial CWV and CWM for traits governing species interactions, as in our case: competitiveness and defense against a predator. We tracked experimental 5-species phytoplankton communities in the presence and absence of a rotifer predator over time. We manipulated the initial community composition so that communities shared at least 3 of the 5 species, but differed in CWV and CWM for defense against predation. We found that species diversity was highest with higher initial trait distributions and that temporal changes in diversity correlated with trait selection. The initial distributions determined the form of selection over time, with directional selection for defense and competitiveness followed by reduced selection and an increase in niche availability when the initial trait distribution was low or high. For intermediate initial trait distributions, we observed directional selection in only one trait followed by stabilizing selection. Differences and changes in selection for defense, competitiveness and species diversity, correlated with the changes in predator density over time. This suggests that the initial trait distribution determined species diversity through a feedback loop with changes in selection on traits and predator density. Overall, our study shows that identifying ecological selection on functional traits can provide a mechanistic understanding of community assembly.
https://doi.org/10.5061/dryad.pvmcvdnvt
Description of the data and file structure
This dataset contains the data required to replicate analyses in Vu & Becks (2024), testing the hypothesis that changes in species diversity over time is affected by selection imposed by predation and that this depended on initial trait distribution. The data covers maximum growth rate and clearance rate measurements for 13 phytoplankton species, as well as the population dynamics for 6 phytoplankton communities.
Files and variables
File: ingestion_rate.txt
Description: We measured the ingestion rate of the rotifer Brachionus calyciflorus as a mean for defense against predation for 13 phytoplankton species with 5 replicates for each species and transformed the ingestion rate into clearance rate to obtain the volume in µL that was cleared by a single rotifer.
Variables
- species: Phytoplankton species names grazed by the rotifer.
- ClearRate: Volume in µL that was cleared by an individual rotifer.
File: max_growth_rate.txt
Description: We measured the maximum growth rate for 13 phytoplankton species with 3 replicates for each species.
Variables
- species: Phytoplankton species names.
- maxGR: Maximum growth rate for each phytoplankton species.
File: data_all_final.txt
Description: This data set contains all data required for the analysis of Vu & Becks (2024). For equal weights of the traits, data on maximum growth rate and ingestion rate were normalized using (x - min(x)) / (max(x) - min(x)).
Variables
- community: Experimental community
- day: Experimental days in numerics
- replicate: Experimental replicates
- species: Phytoplankton species
- p_cells_mL: Specific phytoplankton species density as cells per mL
- p_total_rep: Total phytoplankton density per replicate as cells per mL
- rt_reps_ind_mL: Rotifer density per replicate as individuals per mL
- rt_mean_ind_mL: Mean rotifer density across replicates as individuals per mL
- rt_log_reps: Logarithm of rotifer density per replicate
- rt_log_mean: Logarithm of mean rotifer density across replicates
- rt_gr: Rotifer growth rate
- rt_mean_gr: Mean of rotifer growth rate
- g_mean_sp: Mean maximum growth rate across 3 replicates
- i_mean_sp: Mean clearance rate across 5 replicates
- g_CWM: Community weighted mean for the communities maximum growth rate per replicate
- i_CWM: Community weighted mean for the communities clearance rate per replicate
- g_CWV: Community weighted variance for the communities maximum growth rate per replicate
- i_CWV: Community weighted variance for the communities clearance rate per replicate
- H_max: Maximum Shannon diversity
- H: Shannon diversity index
- E: Shannon equitability index
- H_mean: Mean of Shannon diversity index
- E_mean: Mean of Shannon equitability index
- area_d0: Initial trait space area
- area_d20: Final trait space area
- day_chr: Experimental days in characters
File: data_rep_final.txt
Description: This data set contains the data summarised per replicate required for the analysis of Vu & Becks (2024)
Variables
- community: Experimental community
- day: Experimental day
- replicate: Experimental replicates
- p_mean_mL: Mean phytoplankton density per replicate as cells per mL
- p_total_rep: Total phytoplankton density per replicate as cells per mL
- rt_mean_mL: Mean rotifer density across replicates as individuals per mL
- rt_gr: Rotifer growth rate
- rt_mean_gr: Mean rotifer growth rate
- g_CWM: Community weighted mean for the communities maximum growth rate per replicate
- i_CWM: Community weighted mean for the communities clearance rate per replicate
- g_CWV: Community weighted variance for the communities maximum growth rate per replicate
- i_CWV: Community weighted variance for the communities clearance rate per replicate
- H_max: Maximum Shannon diversity index
- H: Shannon diversity index
- E: Shannon equitability index
- area_d0: Initial trait space area
- area_d20: Final trait space area
- g_CWM_com: Community weighted mean for the communities maximum growth rate across replicates
- i_CWM_com: Community weighted mean for the communities clearance rate across replicates
- g_CWV_com: Community weighted variance for the communities maximum growth rate across replicates
- i_CWV_com: Community weighted variance for the communities clearance rate across replicates
Code/software
All statistical analyses were performed using the software Rstudio (R version 4.2.2., R Core Team, 2022).
The following list of packages are required prior to the analysis:
- library(tidyverse)
- library(rstatix)
- library(ggplot2)
- library(ggpubr)
- library(FSA)
- library(lme4)
- library(effects)
- library(emmeans)