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opencc-zeroApr 2023View details →

Implementation of biotic interactions in niche analyses unravels the patterns underneath community composition in clownfishes

Biotic interactions are key to understanding the ecology of species and communities. As such, integrating biotic interactions into ecological niche modelling methods has been a central topic of research for the last decade. Yet, the role of biotic interactions remains overlooked. Mutualistic systems constitute perfect study cases for analysing the effect of biotic interactions on species niches and communities' composition. Using the clownfish-sea anemone interaction, we integrate mutualistic interactions into a niche quantification framework to analyse the effect of biotic interactions in the estimation of species niches, and competition patterns among clownfish communities. Our results show that ignoring biotic interactions can strongly affect species' ecological niche estimations. More importantly, sea anemones seem to mediate competition among clownfishes, structure communities and allow coexistence in competitive environments. These findings strongly support the importance of biotic interactions in shaping communities. Future studies could use the proposed analytical framework, which could also serve multiple conservation purposes.

opencc-zeroMay 2024View details →

Data and scripts for the colour analysis from: Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish

Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus on Amphiprion clarkii (Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sedentary adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status of A. clarkii has been under debate. We used whole-genome resequencing data of 67 A. clarkii specimens spread across the Indian and Pacific Oceans to characterise the species' population structure, demographic history, and colour polymorphism. We found that A. clarkii spread from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a stepping-stone dispersal and that gene flow was pervasive throughout its demographic history. Interestingly, colour patterns differed noticeably among the Indonesian populations and the two populations at the extreme of the sampling distribution (i.e. Maldives and New Caledonia), which exhibited more comparable colour patterns despite their geographic and genetic distances. Our study emphasises how whole-genome studies can uncover the intricate evolutionary past of wide-ranging species with diverse phenotypes, shedding light on the complex nature of the species concept paradigm.

publicSep 2025View details →

Integrating biotic interactions in niche analyses unravels patterns of community composition in clownfishes

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publicMay 2024View details →

Data and scripts for the colour analysis from: Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish

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opencc-by-4.0Dec 2024View details →

Data and code for: Host-use Drives Convergent Evolution in Clownfish

This folder contains the following files: data/Alignments_WithOutgroups.tar.gz:     Contains the alignments of 10,720 genes with the sequences of the outgroup Pomacentrus moluccensis. The gene IDs correspond to the ID of the Amphiprion frenatus reference genome (Marcionetti et al., 2018; https://datadryad.org/stash/dataset/doi:10.5061/dryad.nv1sv). The position of the gene on the Amphiprion percula chromosomes is also reported. For information on the methods and sample names, please refer to the publication. These alignments were used to infer the species tree with ASTRAL-III. Alignments for the genes selected with SortaDate and used for dating with BEAST are also available and are: chr04_g2455.t1.WithOutgroup.phy, chr05_g51486.t1.WithOutgroup.phychr05_g56452.t1.WithOutgroup.phy, chr08_g50086.t1.WithOutgroup.phy, chr09_g35092.t1.WithOutgroup.phy, chr09_g49030.t1.WithOutgroup.phy, chr10_g47484.t1.WithOutgroup.phy, chr11_g5494.t1.WithOutgroup.phy, chr11_g32313.t1.WithOutgroup.phy, chr12_g7961.t1.WithOutgroup.phy, chr12_g27572.t1.WithOutgroup.phy, chr12_g32580.t1.WithOutgroup.phy, chr13_g33152.t1.WithOutgroup.phy, chr15_g60485.t1.WithOutgroup.phy, chr16_g18013.t1.WithOutgroup.phy, chr17_g60288.t1.WithOutgroup.phy, chr22_g6154.t1.WithOutgroup.phy, chr22_g22141.t1.WithOutgroup.phy, chr22_g29206.t1.WithOutgroup.phy, chr23_g36756.t1.WithOutgroup.phy.   data/DatedTree.WithOutgroup.tree:     BEAST2 output. The clownfish dated phylogenetic tree with the outgroup Pomacentrus moluccensis used for rooting. The tree was obtained with BEAST2, using 20 most informative genes. For each partition, we applied a GTR+ G site model and an uncorrelated relaxed clock with a lognormal distribution. A secondary calibration points was used, setting uniform prior from 10 to 18 MYA for the crown age of clownfishes. For more information on the methods, please refer to the publication.  data/Example.DatFile.evolver.tar.gz:      Templates of the .dat files (MCcodonNSbranchsites.Shifts_to_Entacmaea.dat, MCcodonNSbranchsites.Shifts_to_Radianthus.dat) containing information to simulate sequences with evolver. The two .dat files were used to simulate sequences under different selection scenarios (no positive selection, convergent positive selection, positive selection on "long" or "clade" branches only) during the shifts to Entacmaeae or Radianthus hosts. The files were used with the scripts Create_DATFile_Evolved.Shift_to_Entacmaea.py and Create_DATFile_Evolved.Shift_to_Radianthus.py to generate .dat files for all the conditions, used then in evolver. For more information on the methods, please refer to the publication.  data/DatFiles.Evolver.tar.gz     The .dat files that were obtained for the different omega and evolutionary scenarios, for shifts to Entacmaea and Radianthus hosts. The files are obtained with the template files (Example.DatFile.evolver.tar.gz) and the scripts Create_DATFile_Evolved.Shift_to_Entacmaea.py and Create_DATFile_Evolved.Shift_to_Radianthus.py. The resulting .dat files are run in evolver:         evolverNSbranchsites 6 DAT_FILES.dat      to obtain the codon alignment files to perform power and false positive rate analyses. For more information, please refer to the publication.  data/Alignments_ProteinCodingGenes.tar.gz:      Contains the alignments of the 18,390 protein-coding genes analysed in the study. The gene IDs correspond to the ID of the Amphiprion frenatus reference genome (Marcionetti et al., 2018; https://datadryad.org/stash/dataset/doi:10.5061/dryad.nv1sv). The position of the gene on the Amphiprion percula chromosomes is also reported. For information on the methods and sample names, please refer to the publication. These alignments were used to test for convergent positive selection occurring during host shifts.  data/Example.ControlFiles.CodeML.tar.gz     It contains examples of the control files for the null model (no positive selection, H0), alternative model (positive selection, H1), and the site model M1a (used to verify the correct optimization of the null model). The final control files for each gene and condition (shift to Entacmaea or Readianthus host) were generated with the script Create_CTLFile_CodeML.py.  data/LabelledTree.CodeML.tar.gz     Tree files used in codeml analyses, with shifts to Entacmaea labelled as foreground branches (ClownTree.Rooted.Label_Entacmaea.nwk, ClownTree.Rooted.Label_Entacmaea.NoLongBranches.nwk) and shifts to Radianthus labelled as foreground branches (ClownTree.Rooted.Label_Radianthus.nwk, ClownTree.Rooted.Label_Radianthus.NoLongBranches.nwk). The trees do or do not have the 3 "long branches" species (A. ocellaris, A. percula, P. biaculeatus). For more information, refer to the publication. An additional folder (Additional_labelled_trees_for_test_on_simulated_data.tar.gz) containg the trees with only specific species kept and labelled. These trees were used for codeml analyses on simulated alignments, to investigate false positives and power of the analyses. For more information, refer to the publication.  data/SimulatedData_BranchSite_Results.tar.gz     It contains the results for the branch site model on the simulated data. Each file name reports the simulated scenario (Simulated without positive selection: Simulated_NO_PS_Entacmaea / Simulated_NO_PS_Radianthus; simulated convergent positive selection: Simulated_PS_Entacmaea / Simulated_PS_Radianthus; Simulated positive selection on long branches : Simulated_PS_LongBranches / Simulated_PS_Premnas; Simulated positive selection on "clade" branches: Simulated_PS_AKA / Simulated_PS_Ephi), as well as the tested scenario (Tested for positive selection: Tested_PS_Entacmaea / Tested_PS_Radianthus; or tested for positive selection on specific branches). Each file contains the information on the name of the original file, the simulated scenario, the tested scenario, the simulated omega, the replicate number, the log-likelihood of the tested model (site model: M1a, null model without positive selection: H0, alternative model with positive selection: H1), and the p-values associated to the likelihood-ratio test (LRT_pvalue).  For more information, refer to the publication.  data/EmpiricalData_BranchSite_Results.tar.gz     It contains the results for the branch site model for the 18,390 protein-coding genes tested in the study, for shifts to Entacmaea  (Results.BranchSiteModel.Shifts_To_Entacmaea.txt, Results.BranchSiteModel.Shifts_To_Entacmaea.NoLongBranches.txt) and shifts to Radianthus hosts (Results.BranchSiteModel.Shifts_To_Radianthus.txt, Results.BranchSiteModel.Shifts_To_Radianthus.NoLongBranches.txt). Each file contains information on the chromosome information of the analyzed gene, the name of the gene, the log-likelihood of the M1a model (site model, used to verify the correct optimization of the null model), the log-likelihood of the null model (H0) and the alternative model (H1), and the p-values associated to the likelihood-ratio test (LRT_pvalue). These p-values were subsequentially corrected for multiple testing. For more information, refer to the publication.  data/ASR_adult_host_4st.rds     It contains the results of reproductive host associations ancestral states reconstruction to the form of a list() R object. In the list $joint returns a tree with joint ancestral states (returns the most likely ancestral reproductive host association at nodes), $marginal returns a tree with the likelihood of each state at nodes, $simmap returns 100 stochastic maps of ancestral states along branches of the tree calculated over the marginal reconstruction, $map returns a map of ancestral states along branches estimated from the joint reconstruction. data/Absolute_host_assoc.tar.gz     It contains description of the sources used for characterizing host associations for each species of clownfish. For each species, we provide a list of pictures used from public citizen science databases with associated urls and additional published references if used. reprod_host.csv contains our final classification of reproductive host associations. data/DEC.tar.gz     It contains files used for the biogeographic reconstruction (areas_adjacency_clowns.txt, areas_clowns.txt, calibrated_tree.tre, distances.txt, geo_col.txt) and results of the biogeographic reconstruction. geo_obj.rds is a R object containing the joint reconstruction of ancestral biogeographic states formatted for being used in phylogenetic comparative methods analyses. list_geo_obj.rds is a list of a 100 similar objects generated from stochastic maps of ancestral biogeographic states. data/phenotype.tar.gz     It contains results of clownfish individuals phenotyping. Within each file, the first column is the name of the species identified from the picture. morph_pca.csv contains results of the pca analysis performed on the procrustes of clownfish individuals. morph_traits.csv contains traits values calculated from the prcrustes of clownfish individuals. colorRGB.csv contains results of the pca analysis performed on the concatenated red green and blue channels of each clownfish image. colorWOB.csv contains results of the pca analyses performed independantly on white, orange and black channels. columns with names ending with W represent pca axis generated from white channel (O: orange channel, B: black channel) scripts/Create_CTLFile_CodeML.py:      Script used to generate the codeml control files for codeml analyses (simulated data or empirical data). The scripts needs the path to the folder were the codon alignments (see Alignments_ProteinCodingGenes.tar.gz or Alignments created for simulations) are found, the path were the output file are gonna be written; the path to the alignment, tree file and output as they will be written in the control file; the output suffix.          python Create_CTLFile_CodeML.py PATH/to/Alignments/ PATH/to/out/CTL_files/ alignment_in_ctlFile tree_in_ctlFile path_to_output_in_ctlFile Output_Suffix     This produces the control files of the null model (H0, no positive selection) and alternative model (H1, positive selection), that can be run with codeml         codeml CONTROL_FILE.ctl      to obtain the results. This was done using the tree with shifts to Ratianthus or Entacmaea as foreground branches (see LabelledTree.CodeML.tar.gz). This was also performed on real data or simulated data. For more information, refer to the publication.  scripts/Create_DATFile_Evolved.Shift_to_Entacmaea.py scripts/Create_DATFile_Evolved.Shift_to_Radianthus.py     Scripts used to generate the .dat files for evolver simulations. The scripts need the template .dat files (provided in Example.DatFile.evolver.tar.gz) and the information of the path where to save the resulting .dat files:         python Create_DATFile_Evolved.Shift_to_Entacmaea.py  MCcodonNSbranchsites.Shifts_to_Entacmaea.dat Out_dat_files_Entacmaeae/         python Create_DATFile_Evolved.Shift_to_Radianthus.py  MCcodonNSbranchsites.Shifts_to_Radianthus.dat Out_dat_files_Radianthus/     The .dat files obtained are then run in evolver to generate the simulated alignments:         evolverNSbranchsites 6 DAT_FILES.dat      The simulated alignments and tree were then used in codeml to evaluate power and false positive rate of positive selection analyes. The file Create_CTLFile_CodeML.py was used to create control files and control files were run with codeml. For more information, refer to the publication.  scripts/ASR_adult_host.R     Script used to perform the ancestral state reconstruction of reproductive host assocication. It uses data/Absolute_host_assoc/reprod_host.csv and data/BEAST2.DatedTree.WithOutgroup.tree and outputs the data/ASR_adult_host_4st.rds file. It requires the instalation of a few R packages ("ape", "igraph", "mvMORPH", "scales", "sda", "TeachingDemos","png", "corHMM","phytools") that can be installed with the function (install.packages("package-name"))         Rscript scripts/ASR_adult_host.R scipts/BGB_fit.R     Script used to perform the ancestral state reconstruction of biogeographic region. It uses data embeded into data/DEC.tar.gz and outputs data/geo_obj.rds and data/list_geo_obs.rds. It requires the instalation of a few R packages ("ape","BioGeoBEARS", "GenSA", "FD", "snow", "parallel","cladoRcpp","rexpokit") that can be installed with the function (install.packages("package-name")).         Rscript scripts/BGB_fit.R scripts/PCM_fit.R     Script used to perform the phylogenetic comparative analyses. It uses data embeded into the data folder. First part performs multivariate phylogenetic anova. Second part performs model testing and parameter estimations using multivariate and univariate datasets and ancestral state reconstruction joint maps. Third part performs model testing and parameter estimations using multivariate and univariate datasets and 100 stochastic maps from marginal ancestral state reconstructions. Results are saved into .rds files. It requires the instalation of a few R packages ("ape", "phytools", "mvMORPH", "RPANDA", "geiger","OUwie") that can be installed with the function (install.packages("package-name")).         Rscript scripts/PCM_fit.R scripts/manova_var.R     Script used to estimate uncertainties on the mANOVA that are due to intraspecific variation. It uses data embeded into the data folder. Results are saved into .rds files. It requires the instalation of a few R packages ("ape", "phytools", "mvMORPH", "RPANDA", "geiger","OUwie") that can be installed with the function (install.packages("package-name")).         Rscript scripts/manova_var.R

opencc-by-4.0Dec 2018View details →

Data from: Insights into the genomics of clownfish adaptive radiation: genetic basis of the mutualism with sea anemones

Genomic data of 9 clownfish (Amphiprion akallopisos, A.  bicinctus, A. melanopus, A. nigripes, A. ocellaris, A. preideraion, A. polymnus, A. sebae, Premnas biaculeatus) species and 1 damselfish species (Pomacentrus moluccensis), presented in " Insights into the genomics of clownfish adaptive radiation: genetic basis of the mutualism with sea anemones". For each species, the following files are available: Species_genome.fasta: Genome assembly of the species in fasta format. The genome was obtained using Illumina paired-end reads,  following a reference-based method. For more information, please refer to the publication Species_genome.Annotation.gff3: Structural genome annotation of the species, in gff3 format. Structural annotation was obtained with a combination of ab initio and RNAseq-data based approaches. Fina gene models were obtained with MAKER2. For more information, please refer to the publication Species_genome.proteins.uniprot.fa: Predicted protein sequences from the genome assembly of the species, in fasta format. Each protein is annotated with the best blast hit with SwissProt database. For more information, please refer to the publication Species_genome.transcripts.uniprot.fa: Predicted coding sequences (CDS) from the genome assembly of the species, in fasta format. Each CDS is annotated with the best blast hit with SwissProt database. For more information, please refer to the publication For Amphiprion ocellaris data, additional to the files presented above, we provided as well the secondary results of the genome assembly using a de novo strategy (Aocellaris_GenomeDeNovo.fasta), its structural annotation (Aocellaris_GenomeDeNovo.Annotation.gff3), and its predicted protein (Aocellaris_GenomeDeNovo.proteins.uniprot.fa) and CDS (Aocellaris_GenomeDeNovo.transcripts.uniprot.fa) sequences.  For more information, please refer to the publication

opencc-by-4.0Mar 2023View details →

Clownfish Hosting Anemone Location Data from GBIF

This is a location dataset derived from GBIF location data for the 10 Clownfish hosting anemones. The data was downloaded, filtered, and used to create range maps in R. The species included are: <ol> <li>Cryptodendrum adhaesivum</li> <li>Entacmaea quadricolor</li> <li>Heteractis aurora</li> <li>Heteractis crispa</li> <li>Heteractis magnifica</li> <li>Heteractis malu</li> <li>Macrodactyla doreensis</li> <li>Stichodactyla gigantea</li> <li>Stichodactyla haddoni</li> <li>Stichodactyla mertensii</li> </ol>

opencc-by-4.0Apr 2023View details →

Data from: Insights into the Genomics of Clownfish Adaptive Radiation: the Genomic Substrate of the Diversification

Mitochondrial genome assembly of 9 clownfish (Amphiprion akallopisos, A.  bicinctus, A. melanopus, A. nigripes, A. ocellaris, A. preideraion, A. polymnus, A. sebae, Premnas biaculeatus) species and 1 damselfish species (Pomacentrus moluccensis), presented in "Insights into the genomics of clownfish adaptive radiation: the genomic substrate of the diversification".

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Host identity and symbiotic association affects the genetic and taxonomic diversity of the clownfish-hosting sea anemone microbiome

All eukaryotic life engages in symbioses with a diverse community of bacteria that are essential for performing basic life functions. In many cases, eukaryotic organisms form additional symbioses with other macroscopic eukaryotes. The tightly-linked physical interactions that characterize many macroscopic symbioses creates opportunities for microbial transfer, which likely affects the diversity and function of individual microbiomes, and may ultimately lead to microbiome convergence between distantly related taxa. Here, we sequence the microbiomes of five species of clownfish-hosting sea anemones that co-occur on coral reefs in the Maldives. We test the importance of evolutionary history, clownfish symbiont association, and habitat on the genetic and predicted functional diversity of the microbiome, and explore signals of microbiome convergence in anemone taxa that have evolved symbioses with clownfishes independently. Our data indicate that host identity shapes the majority of the genetic diversity of the clownfish-hosting sea anemone microbiome, but predicted functional microbial diversity analyses demonstrate a convergence among host anemone microbiomes, which reflect increased functional diversity over individuals that do not host clownfishes. Further, we identify up-regulated microbial functions in host anemones that are likely affected by clownfish presence. Taken together our study reveals an even deeper metabolic coupling between clownfishes and their host anemones, and what could be a previously unknown mutualistic benefit to anemones that are symbiotic with clownfishes

opencc-zeroJan 2020View details →

opencc-by-4.0Mar 2024View details →

Data from: Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex

Mitochondrial genome assembly of populations of three clownfish species (Amphiprion akallopisos, A. sandaracinos and A. akallopisos), presented in "Recurrent gene flow events occurred during the diversification of clownfishes of the skunk complex".

opencc-by-4.0Apr 2024View details →

Eluding anemone nematocysts: are clownfish deprived of N-acetylated sugars on their surface?

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FIGURE 14 in The clownfish-hosting sea anemones (Anthozoa: Actiniaria): updated nomenclature, biogeography, and practical field guide.

FIGURE 14. Representative images of Stichodactyla gigantea encompassing a broad range of geographic and phenotypic variation. A) Wide-angle photograph of S. gigantea in shallow water habitat surrounded by stony corals. Note the strongly wavy oral disc and visible mouth (Kimbe Bay, Papua New Guinea). B) Individual with rare vibrant blue/violet body coloration (Kimbe Bay, Papua New Guinea). C) Macro photograph of S. gigantea column, tentacles, and verrucae. Note the thin tentacles, slightly tapered tentacle tips, and verrucae (arrow) that contrast in color with surrounding column (Kimbe Bay, Papua New Guinea. D) Common tan colored individual (Kimbe Bay, Papua New Guinea). E) Macro photograph of S. gigantea tentacles highlighting tapered tentacle tips (Palawan, Philippines). Photographs by Morgan Bennett-Smith.

FIGURE 10 in The clownfish-hosting sea anemones (Anthozoa: Actiniaria): updated nomenclature, biogeography, and practical field guide.

FIGURE 10. Representative images of the magnificent sea anemone Radianthus magnifica encompassing a broad range of geographic and phenotypic variation. A) Wide-angle photograph of stereotypical R. magnifica perched prominently on exposed rocky outcrop with fully visible purple column and pedal disc (Maldives). B) Retracted individual with column curled into a ball leaving only a small tuft of tentacles visible (Kimbe Bay, Papua New Guinea). C) Macro photograph of tentacles. Note the blunt-rounded ends that are all alike and the small "dot" present in the center of the tentacle tip (Fares-Maathodaa, Maldives). D) Cluster of at least four anemones on rocky outcrop (Saudi Arabia, Red Sea). E) Large solitary individual with pink tentacle tips. Note that the oral disc is fully expanded over the substrate obscuring the column and pedal disc from view (Kimbe Bay, Papua New Guinea. Photographs by Morgan Bennett-Smith and Benjamin Titus.

FIGURE 7 in The clownfish-hosting sea anemones (Anthozoa: Actiniaria): updated nomenclature, biogeography, and practical field guide.

FIGURE 7. Confirmed geographic range of Radianthus crispa in the Indo-West Pacific. Red dots represent species observations from the Global Biodiversity Information Facility (GBIF). Blue shaded area represents shallow water habitat (60 m bathymetry).

FIGURE 11 in The clownfish-hosting sea anemones (Anthozoa: Actiniaria): updated nomenclature, biogeography, and practical field guide.

FIGURE 11. Confirmed geographic range of Radianthus magnifica in the Indo-West Pacific. Red dots represent species observations from the Global Biodiversity Information Facility (GBIF). Blue shaded area represents shallow water habitat (60 m bathymetry).

FIGURE 5 in The clownfish-hosting sea anemones (Anthozoa: Actiniaria): updated nomenclature, biogeography, and practical field guide.

FIGURE 5. Confirmed geographic range of Heteractis aurora in the Indo-West Pacific. Red dots represent species observations from the Global Biodiversity Information Facility (GBIF). Blue shaded area represents shallow water habitat (60 m bathymetry).

FIGURE 17 in The clownfish-hosting sea anemones (Anthozoa: Actiniaria): updated nomenclature, biogeography, and practical field guide.

FIGURE 17. Confirmed geographic range of Stichodactyla haddoni in the Indo-West Pacific. Red dots represent species observations from the Global Biodiversity Information Facility (GBIF). Blue shaded area represents shallow water habitat (60 m bathymetry).

FIGURE 13 in The clownfish-hosting sea anemones (Anthozoa: Actiniaria): updated nomenclature, biogeography, and practical field guide.

FIGURE 13. Confirmed geographic range of Radianthus malu in the Indo-West Pacific. Red dots represent species observations from the Global Biodiversity Information Facility (GBIF). Blue shaded area represents shallow water habitat (60 m bathymetry).

FIGURE 3 in The clownfish-hosting sea anemones (Anthozoa: Actiniaria): updated nomenclature, biogeography, and practical field guide.

FIGURE 3. Confirmed geographic range of Entacmaea quadricolor in the Indo-West Pacific. Red dots represent species observations from the Global Biodiversity Information Facility (GBIF). Blue shaded area represents shallow water habitat (60 m bathymetry).