Data from: Same places, same stories? Genomics reveals similar structuring and demographic patterns for four Pocillopora coral species in the southwestern Indian Ocean
Data files
Jan 03, 2024 version files 426.22 MB
-
Command_line_examples.docx
-
Command_line_examples.txt
-
DB_FAMD.txt
-
DB_Pocillopora_connectivity_WIO_1030DNA.csv
-
example.blueprint
-
List_1559SNP_noLD_SpID.txt
-
List_Pacuta_1493SNP_noLD.txt
-
List_Pmeand_1412SNP_noLD.txt
-
List_Pverru_1446SNP_noLD.txt
-
List_Pvillo_1351SNP_noLD.txt
-
Pacuta_246DNA_17440SNP.vcf
-
Pmeand_497DNA_13909SNP.vcf
-
Pocillopora_1030DNA_1559SNP.vcf
-
Pverru_185DNA_14333SNP.vcf
-
Pvillo_102DNA_13167SNP.vcf
-
README.md
Abstract
Aim Efficiently protecting species requires knowing their ecological, life history and reproductive traits. This is particularly decisive for scleractinian corals, key components of coral reefs, which are experiencing critical declines. Yet their connectivity remains insufficiently documented. Here, we focused on four distinct species of the coral genus Pocillopora found in diverse habitats of the southwestern Indian Ocean and presenting various reproductive strategies. We aimed to understand whether these traits affect species connectivity.
Location Archipelagos and islands of the southwestern Indian Ocean.
Taxon Pocillopora spp.
Methods We used target-capture to collect single-nucleotide polymorphisms (SNPs) from over a thousand colonies sampled across nine localities. From the ca. 1,400 SNPs retained per species, Bayesian clustering methods, networks and demographic inferences were applied to first infer the population genetic structure and connectivity of each species, then the demographic history of each population.
Results All four Pocillopora species exhibited almost the same genetic structuring pattern, reflecting the sampled ecoregions (Madagascar and surrounding islands vs. Mascarene Islands). However, the genetic differentiation was stronger ( FST about 10 times higher) for P. acuta, the species inhabiting more enclosed habitats, such as lagoons and shallow waters, and reproducing mainly asexually. Similarly, all populations, except those from P. acuta, showed a signature of population expansion ca. 100,000 years ago, following the penultimate glacial period.
Main conclusions These results indicate reduced gene flow between Madagascar and the Mascarenes, probably linked to currents, suggesting distinct connectivity networks that should be considered independently when setting up conservation plans. In addition, shared demographic histories reflect that populations from these species have probably met the same environmental constraints and reacted similarly, something that should be considered in light of the ongoing rapid climate change.
README
README for data from: Oury N, Mona S, Magalon H (2023) Same places, same stories? Genomics reveals similar structuring and demographic patterns for four Pocillopora coral species in the southwestern Indian Ocean. Journal of Biogeography n/a:1–15. doi: 10.1111/jbi.14788
Available at https://doi.org/10.5061/dryad.pnvx0k6vw.
Data included:
1) Command_line_examples.docx and Command_line_examples.txt contain examples of the command lines used for reads processing and population structure analyses in Oury et al. (2023 - J Biogeogr). These are provided in two different formats for compatibility reasons.
2) DB_FAMD.txt contains the data for the FAMD (one line for each pair of conspecific populations).
Column details:
- Species: Pocillopora species for populations 1 & 2
- Cluster1, Cluster2: Cluster for populations 1 & 2
- Comp: Type of comparison (intra-cluster vs. inter-cluster)
- CompxCluster = column Cluster1 vs. column Cluster2
- Pop1, Pop2: populations 1 & 2
- Dist: Distance at sea (in km) between populations 1 & 2
- The following columns are the environmental parameters (SST: sea surface temperature in °C, Salt: salinity in PSS, Cur: current velocity in m.s-1, Chlor: chlorophyll concentration in mg.m-3) for each population, the differences (Diff) and means (Mean)
- Fst: Fst between populations 1 & 2
3) DB_Pocillopora_connectivity_WIO_1030DNA.csv contains the metadata for the 1,023 Pocillopora colonies + 7 replicates (one line for each colony/replicate).
Column details:
- Sample_Name: Name of the colony
- NCBI_BioSample: Corresponding NCBI BioSample accession number
- Name_Replicate: Unique identifier for replicates
- NCBI_SSR: Corresponding NCBI raw reads accession number
- Included in Oury et al. (2023 - Mol Phylogenet Evol): Indicate colonies previously included in the genomic species delimitation study
- Species: Species
- GSH: Genomic species hypothesis
- MLG: Multi-locus genotype: conspecific colonies with the same number were considered belonging to the same clonal lineage
- Truncated_Dataset: Indicate colonies kept in the truncated datasets
- Cluster: Cluster
- Sampling_Site: Sampling site
- Pop_Retained: Indicate final colonies' populations after merging some sites
4) example.blueprint is an example of blueprint input file for Stairway Plot.
5) List_1559SNP_noLD_SpID.txt is the list of 1559 SNPs retained for the one-SNP dataset in Oury et al (CHR_POS format; one line per SNP).
6) List_Pacuta_1493SNP_noLD.txt, List_Pmeand_1412SNP_noLD.txt, List_Pverru_1446SNP_noLD.txt and List_Pvillo_1351SNP_noLD.txt are the lists of SNPs retained after keeping one SNP per locus for each species (CHR_POS format; one line per SNP).
7) Pocillopora_1030DNA_1559SNP.vcf is the species identification dataset.
8) Pacuta_246DNA_17440SNP.vcf, Pmeand_497DNA_13909SNP.vcf, Pverru_185DNA_14333SNP.vcf and Pvillo_102DNA_13167SNP.vcf are the population structure datasets for each species separately before removing individuals with high proportions of missing data, clones and replicates and before keeping one SNP per locus.