DOI: 10.5061/dryad.wh70rxwx4
title: Data from: Niche breadth and divergence in sympatric cryptic coral species (Pocillopora spp.) across habitats within reefs and among algal symbionts

description: While the presence of morphologically cryptic species is increasingly
 recognized, we still lack a useful understanding of what causes and
 maintains co-occurring cryptic species and its consequences for the
 ecology, evolution, and conservation of communities. We sampled 724
 Pocillopora corals from five habitat zones (the fringing reef, back reef,
 and fore reef at 5 m, 10 m, and 20 m) at four sites around the island of
 Moorea, French Polynesia. Using validated genetic markers, we identified
 six sympatric species of Pocillopora, most of which cannot be reliably
 identified based on morphology: P. meandrina (42.9%), P. tuahiniensis
 (25.1%), P. verrucosa (12.2%), P. acuta (10.4%), P. grandis (7.73%), and
 P. cf. effusa (2.76%). For 423 colonies (58% of the genetically-identified
 hosts), we also used psbAncr or ITS2 markers to identify symbiont species
 (Symbiodiniaceae). The relative abundance of Pocillopora species differed
 across habitats within the reef. Sister taxa P. verrucosa and P.
 tuahiniensis had similar niche breadths and hosted the same specialist
 symbiont species (mostly Cladocopium pacificum) but the former was more
 common in the back reef and the latter more common deeper on the fore
 reef. In contrast, sister taxa P. meandrina and P. grandis had the highest
 niche breadths and overlaps and tended to host the same specialist
 symbiont species (mostly C. latusorum). Pocillopora acuta had the
 narrowest niche breadth and hosted the generalist, and more thermally
 tolerant, Durusdinium gynnii. Overall, there was a positive correlation
 between reef habitat niche breadth and symbiont niche breadth –
 Pocillopora species with a broader habitat niche also had a broader
 symbiont niche. Our results show how fine-scale variation within reefs
 plays an important role in the generation and coexistence of cryptic
 species. The results also have important implications for how niche
 differences affect community resilience, and for the success of coral
 restoration practices, in ways not previously appreciated.
description: # Data from: Niche breadth and divergence in sympatric cryptic coral
 species (Pocillopora spp.) across habitats within reefs and among algal
 symbionts
 [https://doi.org/10.5061/dryad.wh70rxwx4](https://doi.org/10.5061/dryad.wh70rxwx4) All data and R code associated with the manuscript "Niche breadth and divergence in sympatric cryptic coral species (Pocillopora spp.) across habitats within reefs and among algal symbionts". ## Sharing/Access information Links to other publicly accessible locations of the data: * [https://github.com/scottcburgess/niche-breadth-Pocillopora-Symbiodiniaceae](http://...) * [https://zenodo.org/records/12745666](https://zenodo.org/records/12745666) This README.txt file was generated on 2024-Jul-22 by Scott Burgess GENERAL INFORMATION 1\. Title of Dataset: Niche breadth and divergence in sympatric cryptic coral species (Pocillopora spp.) across habitats within reefs and among algal symbionts 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): 2021-2022 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**: * ALGAE.R (This code produces Table 1, Table 3, Table 4, Figure 4, and Figure 6) - DISTRIBUTION.R (This code produces Table 3, Figure 2, Figure 3, Figure S1) * Figure 5.R (This code produces Figure 5) - NICHE.R (This code produces Figure 7, Figure 8) * 257_20230414T204804_DBV_20230415T005314.profiles.absolute.abund_and_meta.csv - 257_20230414T204804_DBV_20230415T005314.profiles.relative.abund_and_meta.csv * 257_20230414T204804_DBV_20230415T005314.seqs.absolute.abund_and_meta.csv - 257_20230414T204804_DBV_20230415T005314.seqs.relative.abund_and_meta.csv * Distribution data.csv - mt_ORF_Organism file.csv * mt_ORF_source-table.csv - psbA_Organism file.csv * psbA_source-table.csv - mtORF Alignment 2021_22 samples.fasta * Cladocopium_psbA_2021_alignment_rooted samples only.fasta - 257_20230414T204804_DBV_20230415T005314.seqs.fasta **2. Relationship between files**: ALGAE.R uses: 257_20230414T204804_DBV_20230415T005314.profiles.relative.abund_and_meta.csv, 257_20230414T204804_DBV_20230415T005314.seqs.relative.abund_and_meta.csv Distribution data.csv DISTRIBUTION.R uses Distribution data.csv Figure 5.R uses: 257_20230414T204804_DBV_20230415T005314.seqs.absolute.abund_and_meta.csv Distribution data.csv 257_20230414T204804_DBV_20230415T005314.seqs.fasta NICHE.R uses: Distribution data.csv 257_20230414T204804_DBV_20230415T005314.seqs.absolute.abund_and_meta.csv **3. Metadata** 257_20230414T204804_DBV_20230415T005314.profiles.absolute.abund_and_meta.csv Output from SymPortal. Absolute abundance of ITS2 Type Profiles. For background, see [https://doi.org/10.1111/1755-0998.13004](https://doi.org/10.1111/1755-0998.13004) (especially section '2.3.6 SymPortal output') 257_20230414T204804_DBV_20230415T005314.profiles.relative.abund_and_meta.csv Output from SymPortal. Relative abundance of ITS2 Type Profiles. For background, see [https://doi.org/10.1111/1755-0998.13004](https://doi.org/10.1111/1755-0998.13004) (especially section '2.3.6 SymPortal output') 257_20230414T204804_DBV_20230415T005314.seqs.absolute.abund_and_meta.csv Output from SymPortal. Absolute abundance of ITS2 DIV sequences. For background, see [https://doi.org/10.1111/1755-0998.13004](https://doi.org/10.1111/1755-0998.13004) (especially section '2.3.6 SymPortal output') 257_20230414T204804_DBV_20230415T005314.seqs.relative.abund_and_meta.csv Output from SymPortal. Relative abundance of ITS2 DIV sequences. For background, see [https://doi.org/10.1111/1755-0998.13004](https://doi.org/10.1111/1755-0998.13004) (especially section '2.3.6 SymPortal output') **Distribution data.csv** For each sample (rows), the depth, site, host ID, and symbiont ID. Trip: Unique identifier for each visit to Moorea Date collected.YYYY-MM-DD: Date the sample was collected in YYYY-MM-DD format. Empty cells indicate no data Preservative: DNA preservative Depth.m: Depth in meters where the sample was collected Site: Site ID where the sample was collected Coral.ID: Unique identifier for each sample Box ID: Box ID where the tissue for each sample is stored at Florida State University. Empty cells indicate no data mtORF.RFLP: The mtORF haplotype, and results from RFLP in the case of haplotype 1, for each sample Cladocopium_species: The species of Cladocopium symbiont hosted in each sample, identified using psbA_ncr. Empty cells indicate no data Cladocopium_clade: The clade of Cladocopium symbiont hosted in each sample, identified in Suppl. Fig. 2 and 3 of the paper. Empty cells indicate no data Plate Number: Plate ID where the DNA for each sample is stored at Florida State University **mt_ORF_Organism file.csv** Organism file for mtORF Alignment 2021_22 samples.fasta showing Pocillopora species identification for each mtORF Sequence ID (sample). **mt_ORF_source-table.csv** Additional data associated with each Sequence ID (sample) in mtORF Alignment 2021_22 samples.fasta **psbA_Organism file.csv** Organism file for Cladocopium_psbA_2021_alignment_rooted samples only.fasta showing Cladocopium species identification for each psbA_ncr Sequence ID (sample). **psbA_source-table.csv** Additional data associated with each Sequence ID (sample) in Cladocopium_psbA_2021_alignment_rooted samples only.fasta **mtORF Alignment 2021_22 samples.fasta** FASTA file of aligned mtORF sequences **Cladocopium_psbA_2021_alignment_rooted samples only.fasta** FASTA file of aligned psbA_ncr sequences **257_20230414T204804_DBV_20230415T005314.seqs.fasta** FASTA file of ITS2 sequences