DOI: 10.5061/dryad.905qfttzp
title: Data from: Myxomycete biodiversity on remote islands of the eastern Indian Ocean: A comparison between the Cocos (Keeling) and Christmas Islands

description: 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.
description: # Data from: Myxomycete biodiversity on remote islands of the eastern
 Indian Ocean: A comparison between the Cocos (Keeling) and Christmas
 Islands
 [https://doi.org/10.5061/dryad.905qfttzp](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](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.csv` and `cocos_sites_main.csv` to 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`, and `mainatoll_mainsites.csv` to perform NMDS ordinations. * **Section 3 (Figure 4):** Comparison between island territories. Loads `iot_species.csv` and `iot_sites.csv` to 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 the `outlier()` 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](mailto:kvernes@une.edu.au)