Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae)

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