DOI: 10.5061/dryad.2bvq83bv8
title: Integrating biotic interactions in niche analyses unravels patterns of community composition in clownfishes

description: Mutualistic interactions play a fundamental role in shaping species
 distributions, driving niche differentiation, and structuring communities.
 Yet their influence on realized niches and patterns of coexistence remains
 poorly understood. In clownfishes, mutualism with sea anemones underpins
 their biogeography and ecological success, with species classified as
 generalists or specialists according to their host specificity. However,
 the extent to which host availability constrains or expands clownfish
 niches has remained unclear. Here we used ecological niche models (ENMs)
 across the Indo-Pacific to examine how host sea anemones shape clownfish
 realized niches and community composition. We integrated occurrence data
 with climatic and habitat predictors and refined estimates by
 incorporating host niches, quantifying changes in niche breadth, position,
 and overlap. We further developed a multilayered framework to account for
 host use within niche quantification, allowing us to assess patterns of
 resource overlap in communities spanning generalist–specialist dynamics.
 Our results reveal that mutualistic associations strongly shape clownfish
 realized niches, with specialists experiencing greater niche constraints
 than generalists due to their reliance on a limited set of hosts. Host
 availability emerges as a key driver of community structure, producing
 high ecological niche overlap among species that is modulated by host
 partitioning. This host-mediated differentiation facilitates coexistence
 by reducing resource overlap, with generalist–specialist contrasts playing
 a central role in sustaining clownfish biodiversity. Our study highlights
 how biotic interactions mediate species ecological niches and shape
 community assembly in an iconic mutualistic system. Beyond clownfishes,
 our framework offers a transferable approach to incorporate interacting
 species into ENMs, improving ecological interpretations and informing
 conservation efforts in biodiversity hotspots and other mutualistic
 systems.
description: Occurrences, environmental variables and all input data for the
 analyses have been collected from online databases and open-source
 datasets.
description: All analyses are done in R. Developed functions are provided in
 form of a package called NINA.
description: # Reference Information ## Provenance for this README *
 File name: README.txt * Authors: Alberto Garcia Jimenez * Other
 contributors: Olivier Broennimann, Antoine Guisan, Théo Gaboriau and
 Nicolas Salamin * Date created: 2023-02-20 * Date modified: 2023-03-30 *
 Date modified: 2025-09-27 ## Dataset Version and Release History * Current
 Version: * Number: 1.1.1 * Date: 2025-09-27 * Persistent identifier: DOI:
 10.5061/dryad.2bvq83bv8 * Summary of changes: Updated files following the
 revision process, including abstract modifications to align with the
 current manuscript version and improved file organization. * Embargo
 Provenance: n/a * Scope of embargo: n/a * Embargo period: n/a ## Dataset
 Attribution and Usage * Dataset Title: Data for the article
 "Integrating biotic interactions in niche analyses unravels the
 patterns underneath community composition in clownfishes" *
 Persistent Identifier:
 [https://doi.org/10.5061/dryad.2bvq83bv8](https://doi.org/10.5061/dryad.2bvq83bv8) * Dataset Contributors: * Creators: Alberto Garcia Jimenez, Olivier Broennimann, Antoine Guisan, Théo Gaboriau and Nicolas Salamin * Date of Issue: 2023-03-30 * Publisher: n/a * License: Use of these data is covered by the following license: * Title: CC0 1.0 Universal (CC0 1.0) * Specification: [https://creativecommons.org/publicdomain/zero/1.0/](https://creativecommons.org/publicdomain/zero/1.0/); the authors respectfully request to be contacted by researchers interested in the re-use of these data so that the possibility of collaboration can be discussed. * Suggested Citations: * Dataset citation: &gt; Garcia Jimenez, Alberto et al. (2023), Integrating biotic interactions in niche analyses unravels the patterns underneath community composition in clownfishes, Dryad, Dataset, [https://doi.org/10.5061/dryad.2bvq83bv8](https://doi.org/10.5061/dryad.2bvq83bv8) * Corresponding publication: &gt; n/a &gt; Contact Information --- * Name: Alberto Garcia Jimenez * Affiliations: Department of Computational Biology, University of Lausanne * ORCID ID: [https://orcid.org/0000-0002-1532-8784](https://orcid.org/0000-0002-1532-8784) * Email: [agarcia26286@gmail.com](mailto:agarcia26286@gmail.com) * Alternate Email: [alberto.garciajimenez@unil.ch](mailto:alberto.garciajimenez@unil.ch) * Alternative Contact: PI * Name: Nicolas Salamin * Affiliations: Department of Computational Biology, University of Lausanne * ORCID ID: [https://orcid.org/0000-0002-3963-4954](https://orcid.org/0000-0002-3963-4954) * Email: [nicolas.salamin@unil.ch](mailto:nicolas.salamin@unil.ch) * Address: Genopode, University of Lausanne, 1015 Lausanne, Switzerland * Contributor ORCID IDs: * Alberto Garcia Jimenez: [https://orcid.org/0000-0002-1532-8784](https://orcid.org/0000-0002-1532-8784) * Olivier Broennimann: [https://orcid.org/0000-0001-9913-3695](https://orcid.org/0000-0001-9913-3695) * Antoine Guisan: [https://orcid.org/0000-0002-3998-4815](https://orcid.org/0000-0002-3998-4815) * Théo Gaboriau: [https://orcid.org/0000-0001-7530-2204](https://orcid.org/0000-0001-7530-2204) * Nicolas Salamin: [https://orcid.org/0000-0002-3963-4954](https://orcid.org/0000-0002-3963-4954) --- # Additional Dataset Metadata ## Dates and Locations * Dates of data collection: Data collected between May 2019 and July 2022 * Sources of data collection: Geo-referenced occurrences were retrieved from GBIF (last reference record: GBIF.org (30 March 2023) GBIF Occurrence Download [https://doi.org/10.15468/dl.7vn4tq](https://doi.org/10.15468/dl.7vn4tq)) Occurrence data sets were obtained from RLS, GBIF, OBIS and Hexacoral (Atlas of Living Australia 2017; GBIF.org 2018; OBIS 2017; Fautin 2008 respectively) Environmental data were obtained from GMED (Basher et al. 2018) and Bio-Oracle (Tyberghein et al. 2012; Assis et al. 2018) using the same resolution and extent for both datasets (0.083 x 0.083 cell size, representing approximately 9,2 km near the equator) and filtered to locations corresponding to the shallow reefs of the Indo-Pacific Ocean plus the epipelagic zone above 50m depth using a map of the locations of warm waters coral reefs from UNEP-WCMC (UNEP-WCMC 2018). The marine provinces and realm delimitations (Figure S1) were obtained from MEOW (Spalding et al. 2007). --- # Methodological Information * Methods of data collection/generation: see manuscript for details --- # Data and File Overview ## Summary Metrics * File count: 67 * Total file size: ~1 GB * Range of individual file sizes: 158 bytes - 150.6 MB * File formats: .csv, .R,  .zip, .RDS ## Table of Contents The contents of this dataset are organized in folders: \- data.zip: folder containing selected environmental variables, defined marine provinces and filtered geo-referenced occurrences of 28 clownfish species and 10 sea anemones species to carry out ENMs. \- scripts.zip: folder containing ordered scripts to run reproduce analyses and results sequentially and scripts to reproduce the main and supplementary figures and tables from the manuscript. \- results.zip: data sets produced as results of the study \- Rdata.zip: R objects in .RDS format inlcuding ENMs and spatial regression models. ## Setup * Unpacking instructions: n/a * Relationships between files/folders: n/a * Recommended software/tools: parentage- RStudio 2021.09.2; R version &gt; 3.6.3 --- # File/Folder Details ## Details for: interaction_matrix.csv * Description: a comma-delimited file containing the interaction information between clownfishes and sea anemones. * Format(s): .csv * Size(s): 1.45 KB * Dimensions: 29 rows x 11 columns * Variables: * species: species name in the form of GENUS_SPECIES (character) * Columns 2 to 11: values of 0 or 1 indicating absence of interaction or mutualistic interaction, respectively, with the species name in the form of GENUS_SPECIES of sea anemones in the header (numeric) * Missing data codes: NA ## Details for: selected_environmental_variables.csv * Description: a comma-delimited file containing the environmental information of the study area. * Format(s): .csv * Size(s): 18.150 MB * Dimensions: 1023560 rows x 10 columns * Variables: * x: decimal Longitude (numeric) * y: decimal Latitude (numeric) * sstmean: Mean Sea Surface Temperature  (°C; numeric) * sstrange: Sea Surface Temperature  Range (°C; numeric) * temperature.range: Temperature mean at bottom (°C; numeric) * nitrate.mean: Nitrate concentration mean (μmol/m3; numeric) * bphosphate: Bottom mean phosphate concentration (μmol/m3; numeric) * chlarange: Chlorophyll concentration range (mg/m3; numeric) * bo2dissolve: Bottom dissolved oxygen concentration range (μmol/m3; numeric) * dissolved.oxygen.mean: Mean water column dissolved oxygen concentration range (μmol/m3; numeric) * parmean: Photosynthetically Active Radiation (μmol m⁻² s⁻¹; numeric) * Missing data codes: NA ## Details for: marine_regions.csv * Description: a comma-delimited file containing the province and real delimitation of the study area. * Format(s): .csv * Size(s): 6.3 MB * Dimensions: 102360 rows x 4 columns * Variables: * x: decimal Longitude (numeric) * y: decimal Latitude (numeric) * province: Province name (character) * realm: Real name (character) * Missing data codes: NA ## Details for: ROU_data.csv, ROU_data_envhost_predictors.csv and ROU_data_corrected.csv * Description: a comma-delimited file containing the results of UUU analyses. * Format(s): .csv * Size(s): 23.73 KB * Dimensions: 108 rows x 36 columns * Variables: * region: Province name (character) * species: species name in the form of GENUS_SPECIES (character) * D: Shoener's D value between the environmental niche and the corrected niche (numeric). 1 - D equals niche dissimilarity. * Centroid_shift: Centroid shift value (numeric) * Environmental_shift: Environmental Shift value (numeric) * Restricted_niche: Unavailable proportion of the niche (numeric). * Occupied_niche: Used proportion of the niche (numeric). * Unexploited_niche: Unoccupied proportion of the niche (numeric). * num_hosts: number of interacting hosts (integer) * p_hosts_shared: Proportion of host use relative to the number of sea anemones present inhabiting the region (numeric). * n.hosts.reg: number of interacting hosts present in the region (integer). * behavior_reg: mutualistic behavior relative to n.host.reg (character). * Restricted_spatial: Unoccupied proportion of the distribution range (numeric). * Occupied_spatial : Used proportion of the distribution range (numeric). * Unexploited_spatial: Unavailable proportion of the distribution range (numeric). * Missing data codes: NA ## Details for: niche_overlaps.csv and niche_overlaps_corrected.csv * Description: a comma-delimited file containing the results of niche overlap analyses. * Format(s): .csv * Size(s): 44 KB * Dimensions: 275 rows x 10 columns * Variables: * region: Province name (character) * spa: species name in the form of GENUS_SPECIES (character) * spb: species name in the form of GENUS_SPECIES (character) * Denv: Niche overlap between spa and spb environmental niches * Dmut: Niche overlap between spa and spb environmental niches after correcting by biotic interactions * Roverlap: Niche overlap between spa and spb environmental niches considering habitat/resource partitioning * shared_hosts: number of shared hosts between spa and spb (integer) * p_host_shared: proportion of shared host between spa and spb (numeric) * interaction: type of interactions (specialist-specialist, generalist-specialists, generalist-generalist) (character) * c_host_shared: category related to the number of shared hosts (none, some, all) (character) * Missing data codes: NA ## Details for: summary_spatial.csv * Description: a comma-delimited file containing the summary of spatial interaction analyses. * Format(s): .csv * Size(s): 3 KB * Dimensions: 18 rows x 27 columns * Variables: * province: Province name (character) * x: average decimal Longitude of the province (numeric) * y: average decimal Latitude of the province(numeric) * amph.richness: average clownfish richness per province (numeric) * anem.richness: average sea anemone richness per province (numeric) * nG: average number of generalists per province (numeric) * nS: average number of specialists per province (numeric) * T.int: average number of potential interactions (numeric) * D.total: average distribution overlap among species (numeric) * H.total: average habitat overlap among species (considering host use) (numeric) * EN.total: average corrected environmental niche overlap among species (numeric) * EC.total: average host-specific niche overlap among species (numeric) * GG: average distribution overlap among generalist species (numeric) * GS: average distribution overlap among generalist-specialist interactions (numeric) * SS: average distribution overlap among specialist species (numeric) * TGG: average number of generalist-generalist interactions * TGS: average number of generalist-specialist interactions * TSS: average number of specialist-specialist interactions * HGG: average habitat overlap among generalist species (considering host use) (numeric) * HGS: average habitat overlap among generalist-specialist interactions (considering host use) (numeric) * HSS: average habitat overlap among specialist species (considering host use) (numeric) * ENGG: average corrected environmental niche overlap among generalist species (numeric) * ENGS: average corrected environmental niche overlap among generalist-specialist interactions (numeric) * ENSS: average corrected environmental niche overlap among specialist species (numeric) * ECGG: average host-specific niche overlap among generalist species (numeric) * ECGS: average host-specific niche overlap among generalist-specialist interactions (numeric) * ECSS: average host-specific niche overlap among specialist species (numeric) * Missing data codes: NA ## Details for: spatial_results.csv * Description: a comma-delimited file containing the results of the spatial interaction analyses. * Format(s): .csv * Size(s): 23.3 MB * Dimensions: 75151 rows x 27 columns * Variables: * province: Province name (character) * x: decimal Longitude of the province (numeric) * y: decimal Latitude of the province(numeric) * amph.richness: clownfish richness per province (numeric) * anem.richness: sea anemone richness per province (numeric) * nG: number of generalists per province (numeric) * nS: number of specialists per province (numeric) * T.int: number of potential interactions (numeric) * D.total: distribution overlap among species (numeric) * H.total: habitat overlap among species (considering host use) (numeric) * EN.total: corrected environmental niche overlap among species (numeric) * EC.total: host-specific niche overlap among species (numeric) * GG: distribution overlap among generalist species (numeric) * GS: distribution overlap among generalist-specialist interactions (numeric) * SS: distribution overlap among specialist species (numeric) * TGG: number of generalist-generalist interactions * TGS: number of generalist-specialist interactions * TSS: number of specialist-specialist interactions * HGG: habitat overlap among generalist species (considering host use) (numeric) * HGS: habitat overlap among generalist-specialist interactions (considering host use) (numeric) * HSS: habitat overlap among specialist species (considering host use) (numeric) * ENGG: corrected environmental niche overlap among generalist species (numeric) * ENGS: corrected environmental niche overlap among generalist-specialist interactions (numeric) * ENSS: corrected environmental niche overlap among specialist species (numeric) * ECGG: host-specific niche overlap among generalist species (numeric) * ECGS: host-specific niche overlap among generalist-specialist interactions (numeric) * ECSS: host-specific niche overlap among specialist species (numeric) * Missing data codes: NA ## Details for: GG_spatGLMmodel_predictions.csv * Description: a comma-delimited file containing the model predictions and the CI of the host-specific niche overlap in response to species richness and environmental niche overlap in generalist-generalist interactions. * Format(s): .csv * Size(s): 45 KB * Dimensions: 625 rows x 5 columns * Variables: * nG: number of generalist species (integer) * ENGG: environmental niche overlap (numberic) * predicted: predicted host-specific niche overlap (numberic) * fixefVar_0.025: Confidence interval lower threshold (numberic) * fixefVar_0.975: Confidence interval higher threshold (numberic) * Missing data codes: NA ## Details for: GS_spatGLMmodel_predictions.csv * Description: a comma-delimited file containing the model predictions and the CI of the host-specific niche overlap in response to species richness and environmental niche overlap in generalist-specialist interactions. * Format(s): .csv * Size(s): 48 KB * Dimensions: 625 rows x 5 columns * Variables: * amph.richness: number of species (integer) * ENGS: environmental niche overlap (numberic) * predicted: predicted host-specific niche overlap (numberic) * fixefVar_0.025: Confidence interval lower threshold (numberic) * fixefVar_0.975: Confidence interval higher threshold (numberic) * Missing data codes: NA ## Details for: SS_spatGLMmodel_predictions.csv * Description: a comma-delimited file containing the model predictions and the CI of the host-specific niche overlap in response to species richness and environmental niche overlap in specialist-specialist interactions. * Format(s): .csv * Size(s): 47 KB * Dimensions: 625 rows x 5 columns * Variables: * nS: number of specialist species (integer) * ENSS: environmental niche overlap (numberic) * predicted: predicted host-specific niche overlap (numberic) * fixefVar_0.025: Confidence interval lower threshold (numberic) * fixefVar_0.975: Confidence interval higher threshold (numberic) * Missing data codes: NA ## Details for: overall_spatGLMmodel_predictions.csv * Description: a comma-delimited file containing the model predictions and the CI of the host-specific niche overlap in response to species richness and environmental niche overlap in all types of interactions. * Format(s): .csv * Size(s): 45 KB * Dimensions: 625 rows x 5 columns * Variables: * amph.richness: number of generalist species (integer) * EN.Total: environmental niche overlap (numberic) * predicted: predicted host-specific niche overlap (numberic) * fixefVar_0.025: Confidence interval lower threshold (numberic) * fixefVar_0.975: Confidence interval higher threshold (numberic) * Missing data codes: NA ## Description of the script files and structure 0 indexed scripts are preliminary filtering and data manipulation. Shared input data sets are the result of those scripts. 1_reg_models.R carries out the PCA-based ENMs and the mutualism-refiend model 2_ROU_analysis.R estimates the ROU metrics to compare the ecological niche with the mutualism-refined niche and assess the impact of biotic interactions. This script outputs the file *'*ROU_data.csv'. 3_nicheOverlaps.R estimates the niche overlap among clownfish species at a province level and outputs the file 'niche_overlaps.csv' 4_spatialCompetition.R will compute the spatial distributions of the different niche overlaps and also subsetting them by the type of interactions. This script will output the files 'spatial_results.csv' and 'summary_spatial.csv', where the former is the information per location and the latter is the averaged values per province. GLM_and_moranItests.R runs Generalized Linear Models and explores the spatial autocorrelation of the 'spatial_results.csv' data set. spatialGLMM.R runs spatial Generalized Linear Mixed Models and creates model predictions for a surface plot shown in Figure S8. It will output the files 'overall_spatGLMmodel.csv', 'GG_spatGLMmodel.csv', 'GS_spatGLMmodel.csv', and 'SS_spatGLMmodel.csv' containing the models' results that are used in the script 'TableS4.R' to create the table, and the files 'overall_spatGLMmodel_predictions.csv', 'GG_spatGLMmodel_predictions.csv', 'GS_spatGLMmodel_predictions.csv', and 'SS_spatGLMmodel_predictions.csv' containing the data set with the predictions to plot running the script FigureS8.R All main figures and supplementary figures can be obtained by running the script 'figureX.R'. For tables, run 'TablesX.R'. Other scripts with additional models tested and analyses performed during revision are also provided in scripts. ## Code/Software These analyses are run in R and require the installation of certain packages, all available in CRAN repositories. The main functions used in this study are custom-made and provided in the script 'functions.R'. --- END of README