Data from: Niche breadth and divergence in sympatric cryptic coral species (Pocillopora spp.) across habitats within reefs and among algal symbionts
Data files
Aug 06, 2024 version files 2.48 MB
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257_20230414T204804_DBV_20230415T005314.profiles.absolute.abund_and_meta.csv
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257_20230414T204804_DBV_20230415T005314.profiles.relative.abund_and_meta.csv
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257_20230414T204804_DBV_20230415T005314.seqs.absolute.abund_and_meta.csv
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257_20230414T204804_DBV_20230415T005314.seqs.fasta
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257_20230414T204804_DBV_20230415T005314.seqs.relative.abund_and_meta.csv
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ALGAE.R
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Cladocopium_psbA_2021_alignment_rooted_samples_only.fasta
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Distribution_data.csv
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DISTRIBUTION.R
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Figure_5.R
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mt_ORF_Organism_file.csv
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mt_ORF_source-table.csv
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mtORF_Alignment_2021_22_samples.fasta
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NICHE.R
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psbA_Organism_file.csv
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psbA_source-table.csv
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README.md
Abstract
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.
README: 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
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
- 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 (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 (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 (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 (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