Rates of species turnover across elevation vary with vertical stratum in rainforest ant assemblages
Cite this dataset
Leahy, Lily; Scheffers, Brett; Andersen, Alan; Williams, Stephen (2023). Rates of species turnover across elevation vary with vertical stratum in rainforest ant assemblages [Dataset]. Dryad. https://doi.org/10.5061/dryad.59zw3r2fn
Abstract
Climatic variation at local scales can influence both exposure and sensitivity of organisms and thereby scale up to influence population persistence and community composition across broader geographic extents. Tropical forest canopies are more climatically dynamic than the understorey. Consequently, the niche space of forest canopies has higher overlap in thermal conditions along elevation gradients, which imposes less of a climatic barrier to arboreal species than their ground-dwelling counterparts. We use ant communities of the Australian Wet Tropics to test the prediction that ground communities should have higher rates of species turnover over elevation compared to arboreal communities. We sampled ground and arboreal ants along elevation gradients at a bioregional scale that includes four mountain sub-regions. We assessed community composition at three spatial resolutions (regional, elevation, vertical) and then calculated beta diversity (species turnover) over elevation for ground and arboreal communities using null modelling procedures to compare different-sized species pools. Vertical niche affinity was a strong contributor to overall biogeographic patterns; indicated by a strong interaction between vertical niche and elevation in beta diversity models. On average, the ground community exhibited a pronounced elevational distance-decay pattern while the arboreal community showed no pattern. Mean species turnover was 36% higher in ground than arboreal communities. Our findings suggest that the vertical niche has a pronounced effect on biogeographic patterns which has important implications for understanding the role of local scale climate conditions in shaping communities and for potential responses to future climate change.
README: Rates of species turnover across elevation vary with vertical stratum in rainforest ant assemblages
https://doi.org/10.5061/dryad.59zw3r2fn
The folder Leahy_etal_DataS1 contains the data and R scripts for the article. All material is free to use, but we would appreciate being informed by email if the data is used and this dataset and article cited if appropriate. Questions or comments can be addressed to Lily Leahy: l.leahy@latrobe.edu.au
Description of the data and file structure
File list (files found within DataS1.zip)
- Leahy_etal_WFCA_Ant_Data.csv
- Leahy_etal_beta_div.csv
- Leahy_etal_Ant_Species_Composition.R
- Leahy_etal_Ant_Beta_Diversity.R
- Leahy_etal_Models.R
Description of files and workflow
Have all files in the same folder and set R working directory to this folder.
Leahy_etal_WFCA_Ant_Data.csv
Main survey collections data in a site by species matrix showing all data for all sites surveyed. Tuna baited vials were placed every three metres from ground to canopy in trees at 15 elevation sites at four subregion mountain ranges of the Australian Wet Tropics Bioregion. Cells of site by species matrix are counts of each species per vial, note downstream analyses use species occurrence. Note, the data file includes empty vials that lacked ants. mtn = Mountain Subregion (Atherton = AU, Carbine = CU, Windsor = WU, Finnegan = FU), ele = Elevation m asl, tree = survey tree number (1-5), height = vertical survey height (0 = ground, 3-27m = arboreal), vial = baited vial number/code.
Leahy_etal_beta_div.csv
This data is produced in the R script Leahy_etal_Ant_Beta_Diversity.R and used for modelling in the R script Leahy_etal_Models.R. mtn = mountain subregion as above, niche = vertical niche (ground, arboreal), pairwise = the pairwise site numbers, (e.g. AU 2_1 represents Atherton site 400m asl compared to Atherton site 200m asl), dist = elevational distance between two sites. sim, sne, sor = observed beta diversity metrics. SESsim, SESsne, SESsor = null model beta diversity metrics.
Leahy_etal_Ant_Species_Composition.R
R file for analysis of species composition patterns across sub-region, elevation, and vertical height. Read in Leahy_etal_WFCA_Ant_Data.csv.
Script includes: data wrangling to get into correct format, nMDS, checking of multivariate dispersion, PERMANOVA model, production of nMDS figures.
Leahy_etal_Ant_Beta_Diversity.R
R file for analysis of beta diversity (species turnover) within each sub-region amongst elevation sites. Read in Leahy_etal_WFCA_Ant_Data.csv. Species are allocated to ground or arboreal assemblage based on frequency of occurrence. Beta diversity is analysed separately for ground and arboreal assemblages. Analysis of beta diversity implements package BETAPART ver. 1.5.2. Note, all three metrics Bsim, Bsne, Bsor, are calculated but only Bsim, which represents species turnover, is used in downstream analyses and models. Null modelling procedure and observed beta diversity metrics calculated calculated in a for loop for each subregion and vertical assemblage and then collated at the end.
Writes a csv file titled: Leahy_etal_beta_div.csv
This file is read in for use in the next R script Leahy_etal_Models.R. Can run this script and save the resulting csv or can use the csv Leahy_etal_beta_div.csv already in the folder.
Leahy_etal_Models.R
R file for generalised linear models and analysis of elevational distance decay. Read in Leahy_etal_WFCA_Ant_Data.csv and Leahy_etal_beta_div.csv. Bsim metric of beta diversity (species turnover) is modelled as a function of the interaction between vertical assemblage and elevational distance with a glm model. Pseudo P-values are calculated using a Monte Carlo simulation. Wilcoxon rank sum tests are performed to analyse the difference in mean Bsim of ground versus arboreal assemblages. Figures from model outputs.
Sharing/Access information
Data were also used in the article: Leahy et al. 2021 Vertical niche and elevation range size in tropical ants: implications for climate resilience. Diversity and Distributions 27: 485-496
That data is stored in the Dryad repository below:
Code/Software
All code are R files. Packages and code were originally run with early release version of R and tested to run with up to R version 4.1.1. Citations and versions for relevant R packages in the text of the article.
Methods
Ants were sampled at 15 elevation sites at four mountain sub-regions in the Australian Wet Tropics Bioregion. Ants were collected using tuna baits with 5 vials placed every three metres in vertical height from the ground to the canopy at mutliple trees per site. Survey height varied between 15–27m.
Leahy_etal_WFCA_Ant_Data.csv
The main data file. A site by species matrix. Cells show counts of individuals of each species per vial. This file is read in to the three R scripts in the folder.
Leahy_etal_beta_div.csv
The file produced from the R script "Leahy_etal_Ant_Beta_Diversity.R" that is read in for the models R script, "Leahy_etal_Models"
Funding
The Explorers Club, Student Research Funding
Wet Tropics Management Authority, Student research fund
Skyrail Rainforest Foundation, Research Grant Award
Holsworth Wildlife Research Endowment, Student award
Alfred P. Sloan Foundation, Sloan Research Fellowship