DOI: 10.5061/dryad.pnvx0k6vw
title: Data from: Same places, same stories? Genomics reveals similar structuring and demographic patterns for four Pocillopora coral species in the southwestern Indian Ocean

description: 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.
description: 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
 . 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.