Repository of supplemetal tables, figures, materials, and scripts for the paper "Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development" Kira E. Turnham, Drew C. Wham, Eugenia Sampayo, and Todd C. LaJeunesse.
The ISME Journal DOI: 10.1038/s41396-021-01007-8
## Files overview
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Table_S1_samples.pdf List of Cladocopium samples with corresponding species names, ITS2 designations, host Pocillopora species, country of origin, collection site, and approximate latitude/longitude coordinates.
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Supplemental_Tables_S2-S4.pdf
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- S2. PCR primers and associated references for mitochondrial, nuclear, chloroplast genes and non-coding regions
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- S3. Cladocopium microsatellite loci used in this study and corresponding allele size ranges, repeat motifs, annealing temperatures, and references
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- S4. Cell size differences between Cladocopium pacificum and C.latusorum from Pocillopora host samples obtained in Palau. The mean length and width of ovate cells are listed based off of individual measurements of 55-110 cells per sample
- Supplemental_Figures_S1_S2.pdf
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- S1. Genotype accumulation boxplot showing the percent of unique multilocus genotypes recovered for A) Cladocopium latusorum and B) C. pacificum based on increasing numbers of loci subsampled from the total dataset of 8 loci. Bars represent 95% confidence intervals.
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- S2. Multi-locus genotypes analyzed via STRUCTURE plot showing no overlap between C. latusorum and C. pacificum at K=3 and K=4. Partitioning of each species to these higher K values shows within-species subdivision. Further analyses, beyond the scope of this work, are needed to more accurately assess within-species population genetic structure.
- Supplemental_Dataset_S_concatenated_alignment.nex Cladocopium concatenated nexus alignment: ITS2 LSU cp23S cob cox1
- Supplemental_Dataset_psbA_alignment.nex Cladocopium psbA nexus alignment
- psba_alignment_mol_clock.nex Cladocopium psbA nexus alignment used in molecular clock analyses (contains Cladocopium associated with sibling species Porites panamensis from Eastern Pacific and Porites porites var. colonensi from Western Atlantic
- mr_model_test_output.txt MrModelTest output containing Akaike Information Criterion
Allele freqeuncy, STRUCUTRE, and t-SNE plots were created using PlotSTR, BayesAllele, and t-SNE scripts developed by Drew Wham and available at https://github.com/DrewWham/theclonalescnet (see also Wham et al., 2016).
- Supplemental_Dataset_microsatellites.docx C. pacificum and C. latusorum multi-locus genotypes
- Supplemental_Dataset_linkage.txt Linkage disequilibrium analysis between pairs of all microsatellite loci used for multi-locus genotyping performed using Genepop on the Web https://genepop.curtin.edu.au/)
- PCA_TSNE_and_GMM_script.R Script for performing principal components analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and Gaussian Mixture Model (GMM) clustering analyses
- bayesallele_frequency.Rmd Script for allele frequency based on BayesAllele
- structureplot_K2.Rmd Script for STRUCTURE using PlotSTR