GENERAL INFORMATION 1. Title of Dataset: Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae) 2. Author Information A. Principal Investigator Contact Information Name: Scott Burgess Institution: Florida State University Address: 319 Stadium Drive, Tallahassee, FL, USA 32306 Email: sburgess@bio.fsu.edu 3. Date of data collection (single date, range, approximate date): 2019-08 4. Geographic location of data collection: Moorea, French Polynesia 5. Information about funding sources that supported the collection of the data: National Science Foundation (NSF; OCE-1829867) DATA & FILE OVERVIEW 1. File List: Figure 2 Make.R Figure 4 Make.R Figure 5b Make.R Figure 6 Make.R Figure 1 SNAPP species tree.xml Figure 2.txt Figure 2.vcf Figure 3b - Pocillopora mt genomes.nex Figure 4 and 6 data.csv Figure 4 colors.csv Figure 5a - Cladocopium_psbA.nex Figure 5b - Clad clades.csv Figure 5b_Cladocopium.nex Figure 5b_Pocillopora.nex Figure 5b.csv 2. Relationship between files: Figure 2 Make.R uses Figure 2.txt and Figure 2.vcf Figure 4 Make.R uses Figure 4 and 6 data.csv and Figure 4 colors.csv Figure 5b Make.R uses Figure 5b - Clad clades.csv, Figure 5b_Cladocopium.nex, Figure 5b_Pocillopora.nex, and Figure 5b.csv Figure 6 Make.R Figure 4 and 6 data.csv 3. Metadata Figure 2 Make.R: R code to produce Figure 2, and the accompanying analyses presented in the text, in: Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae). Uses 'Figure 2.txt', 'Figure 2.vcf' Figure 4 Make.R: R code to produce Figure 4, and the accompanying analyses presented in the text, in: Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae). Uses 'Figure 4 and 4 data.csv', 'Figure 4 colors' Figure 5b Make.R: R code to produce Figure 5b, and the accompanying analyses presented in the text, in: Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae). Uses 'Figure 5b - Clad clades.csv', 'Figure 5b_Cladocopium.nex', 'Figure 5b_Pocillopora.nex', 'Figure 5b.csv' Figure 6 Make.R: R code to produce Figure 6, and the accompanying analyses presented in the text, in: Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae). Uses 'Figure 4 and 6 data.csv' Figure 1 SNAPP species tree.xml: Data for species tree used in Figure 1 Figure 2.txt: Metadata Sample_ID: Sample ID Hap_Spp: Pocillopora species or haplotype Figure 2.vcf: Linked dataset of 7,887 SNPs Figure 3b - Pocillopora mt genomes.nex: Nexus tree of Pocillopora mitochondrial genomes used in Figure 3b Figure 4 and 6 data.csv: Metadata Species.haplotype: Pocillopora species or haplotype Depth.m: Sampling depth in meters Site: Sampling site, label corresponds to the site used in the Moorea Coral Reef Long-Term Ecological Research (MCR-LTER) program. Coral.ID: Coral colony identifier Type_profile: ITS2 type profile generated by SymPortal Type_profile_Prop: Proportion of that given ITS2 type profile in colony sampled Remaining columns: Proportion of ITS2 sequences in colony sampled Figure 4 colors.csv: Metadata my_colors: Custom colors for each ITS2 sequence Symbio.clade: ITS2 sequences Figure 5a - Cladocopium_psbA.nex: Nexus tree of Cladocopium taxa in figure 5a Figure 5b - Clad clades.csv: Metadata UCI_links: Sample ID that contains Pocillopora species or haplotype, sample ID, and ITS2 type profile Clad_clades: Clade assignment from figure 5a Figure 5b_Cladocopium.nex: Nexus tree of Cladocopium taxa in Figure 5b Figure 5b_Pocillopora.nex: Nexus tree of Pocillopora taxa used in PACo analysis, Figure 5b Figure 5b.csv: Matrix of Pocillopora host and Cladocopium symbiont links