DOI: 10.5281/zenodo.6710608
title: Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae)

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