Data from: Myxomycete biodiversity on remote islands of the eastern Indian Ocean: A comparison between the Cocos (Keeling) and Christmas Islands
Data files
Oct 23, 2025 version files 69.39 KB
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cocos_sites_main.csv
4.40 KB
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cocos_species_main.csv
5.08 KB
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iot_sites.csv
13.01 KB
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iot_species.csv
18.02 KB
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keeling_sites.csv
1.75 KB
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keeling_species.csv
1.48 KB
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mainatoll_mainsites.csv
2.71 KB
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mainatoll_mainspecies.csv
2.89 KB
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R-code_Stephenson_etal.R
12.89 KB
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README.md
7.14 KB
Abstract
Myxomycetes are a widespread group of organisms, but given their inconspicuousness and the specialist knowledge needed to culture and identify them, there are many regions of the world where they have never been studied. The Cocos (Keeling) Islands, an Australian Territory in the Indian Ocean, are one such location. We collected substrates from islands in the Cocos archipelago, and cultured 37 morphospecies of myxomycete representing 15 genera. Five substrate types were sampled; the greatest species richness was associated with aerial litter, aerial twigs, and ground litter. Eight habitat types were sampled, of which the coconut forest had the greatest species richness. The main (southern) atoll of the Cocos group is dominated by (largely) anthropogenic coconut (Cocos nucifera) forest. Here, there was no relationship between myxomycete community structure and habitat, but substrate type significantly influenced community structure. In contrast, on the northern atoll of Pulu Keeling, which retains a more natural vegetation structure, including large stands of Pisonia grandis forest absent from the southern atoll, there was a strong relationship between the myxomycete community and habitat type but not substrate. We also compared myxomycete diversity from the Cocos Islands with diversity from a similar study of myxomycete morphospecies recorded from Christmas Island. Although 1000 km apart, these are the closest terrestrial habitats in a vast expanse of the eastern Indian Ocean. These islands had very different myxomycete communities and shared relatively few species in common, likely a result of their very different histories, geographies, and contrasting habitat types and substrates available to myxomycetes.
https://doi.org/10.5061/dryad.905qfttzp
Description of the data and file structure
This dataset contains the species occurrence data and analytical code for the manuscript "Myxomycete biodiversity on remote islands of the eastern Indian Ocean: A comparison between the Cocos (Keeling) and Christmas islands" (Biotropica, Manuscript ID: BITR-25-021).
The data and analyses are presented in two parts. The first part describes the myxomycete biodiversity of the Cocos (Keeling) Islands, based on new collections. The second part compares these new data with a previously published dataset from nearby Christmas Island.
All data files and the R script are provided in a single directory, intended for use within the R project 'cocos.Rproj'.
Part 1: Cocos (Keeling) Islands Data
These files contain the data collected specifically for this study from the Cocos (Keeling) Islands, which is divided into the northern atoll (Pulu Keeling) and the southern Main Atoll. Data files are in comma-separated value (.csv) format. For all species files, each row represents a single sample, and each column represents a myxomycete taxon. The values in the cells are counts of occurrences.
File: cocos_species_main.csv
Description: The primary species abundance matrix for all 66 samples collected within the Cocos (Keeling) Islands (Main Atoll and Pulu Keeling combined). Each of the 37 columns represents a myxomycete taxon present in the Cocos (Keeling) Islands.
File: cocos_sites_main.csv
Description: The primary environmental metadata for the 66 samples collected within the Cocos (Keeling) Islands. This file is the direct companion to cocos_species_main.csv.
- Site: A unique numeric or alphanumeric identifier for the sampling location.
- Island: The specific island where the sample was collected (e.g., South Island, Pulu Blan, Pulu Keeling).
- Habitat: The dominant vegetation type at the sample site.
- Substrate: The type of material from which the sample was collected (e.g., aerial litter, ground litter, coconut husks).
- Combo: A concatenated code representing the Habitat and Substrate.
- Island_Group: A categorical variable grouping sites into 'Main Atoll' or 'Pulu Keeling'.
- Island_Veg: A concatenated code representing the Island Group and Habitat.
File: keeling_species.csv
Description: A subset of cocos_species_main.csv, containing the species abundance matrix for the 22 samples from the northern atoll, Pulu Keeling. Each of the 23 columns represents a myxomycete taxon present in Pulu Keeling.
File: keeling_sites.csv
Description: Environmental metadata for the 22 samples collected only within the Pulu Keeling National Park. This is a subset of cocos_sites_main.csv and is the direct companion to keeling_species.csv.
File: mainatoll_mainspecies.csv
Description: A subset of cocos_species_main.csv, containing the species abundance matrix for the 36 samples from the southern Main Atoll used in the final analysis. Each of the 31 columns represents a myxomycete taxon present in the Main Atoll.
File: mainatoll_mainsites.csv
Description: Environmental metadata for the 36 samples collected within the Main Atoll that were used in the final analysis. This is a subset of cocos_sites_main.csv and is the direct companion to mainatoll_mainspecies.csv.
Part 2: Combined Islands Data (Cocos & Christmas)
These files combine the Cocos (Keeling) Islands data described above with previously published data from Christmas Island to allow for a direct comparison between the two island territories. The Christmas Island data were originally published in:
Stephenson, S. L., and B. C. Stephenson. 2019. Distribution and ecology of myxomycetes on Christmas Island, Indian Ocean. Phytotaxa 416(2): 138–148. https://doi.org/10.11646/phytotaxa.416.2.2
File: iot_species.csv
Description: The complete species abundance matrix for all 128 samples from both island groups (66 from Cocos, 62 from Christmas Island). Each of the 68 columns represents a myxomycete taxon. Cell values are counts.
File: iot_sites.csv
Description: The complete environmental metadata for all 128 samples. Each row corresponds to a row in iot_species.csv.
- Site: A unique numeric or alphanumeric identifier for the sampling location.
- Island: The specific island where the sample was collected (e.g., South Island, Pulu Keeling, Christmas Island).
- Habitat: The dominant vegetation type at the sample site.
- Substrate: The type of material from which the sample was collected (e.g., aerial litter, ground litter, bark).
- Combo: A concatenated code representing the Habitat and Substrate.
- Island_Group: A categorical variable grouping sites into 'Main Atoll', 'Pulu Keeling', or 'Christmas'.
- Island_Veg: A concatenated code representing the Island and Habitat.
- IOT: The primary grouping variable for the main analysis: 'Cocos (Keeling) Islands' or 'Christmas Island'.
- IOT2: A finer-scale grouping variable distinguishing the Main Atoll from Pulu Keeling.
R Script
File: R-code_Stephenson_etal.R
Description: This script performs all the statistical analyses and generates the figures (Figures 2, 3, and 4) presented in the manuscript. More detailed comments can be found within the script itself.
- Section 1 (Figure 2): Analysis of Cocos (Keeling) Islands data. Loads
cocos_species_main.csvandcocos_sites_main.csvto calculate and plot species accumulation curves. - Section 2 (Figure 3): Comparison within the Cocos (Keeling) Islands. Loads
keeling_species.csv,keeling_sites.csv,mainatoll_mainspecies.csv, andmainatoll_mainsites.csvto perform NMDS ordinations. - Section 3 (Figure 4): Comparison between island territories. Loads
iot_species.csvandiot_sites.csvto perform an NMDS ordination, PERMANOVA, and SIMPER analyses.
Code/software
All analyses were performed in R (R version 4. x.x is recommended). The script relies on the following packages, which must be installed:
vegan(for all community ecology analyses, including NMDS, PERMANOVA, envfit, specaccum)dave(for theoutlier()function; NOTE: this is an archived package and may require a specific installation procedure.pairwiseAdonis(for pairwise PERMANOVA comparisons)dplyr,tidyr,writexl(for general data manipulation)
Access information
The data and code are provided to fully reproduce the analyses presented in Stephenson et al., "Myxomycete biodiversity on remote islands of the eastern Indian Ocean: A comparison between the Cocos (Keeling) and Christmas islands".
Contact for this dataset:
- Name: Karl Vernes
- Institution: University of New England, Armidale, NSW. Australia.
- Email: kvernes@une.edu.au