DOI: 10.5061/dryad.73kc6
title: Data from: Population genomics meet Lagrangian simulations: oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas

description: Connectivity between populations is a key factor that influences both
 their dynamics and the genetic structuring of marine species. In this
 study, we explored connectivity patterns of a long-dispersing species, the
 edible common sea urchin Paracentrotus lividus, focusing mainly on the
 Adriatic-Ionian basins. We applied a multidisciplinary approach
 integrating population genomics, based on 1122 Single Nucleotide
 Polymorphisms (SNPs) obtained by 2b-RAD in 275 samples, with Lagrangian
 simulations performed with a biophysical model of larval dispersal. We
 detected genetic homogeneity among eight population samples spanning about
 600 km and collected in the focal area (Adriatic-Ionian basins), whereas
 weak but significant differentiation was found with respect to comparative
 samples taken from French and Tunisian coasts. Genetic analyses performed
 separately with putatively neutral and outlier loci confirmed genetic
 homogeneity within Adriatic-Ionian basins, but showed a much higher
 differentiation at the large scale. Lagrangian simulations found a
 significant potential for larval exchange among the eight Adriatic-Ionian
 locations, supporting the view of strong connectivity of P. lividus
 populations in this area. A peculiar pattern emerged from the comparison
 of our results with those obtained from published P. lividus cytochrome b
 (cytb) sequences, which revealed genetic differentiation in the same area
 despite a smaller sample size and a lower power to detect differences.
 Comparison with studies conducted in the same Adriatic-Ionian locations
 using nuclear markers on other species having similar pelagic larval
 durations highlights differences both in realized and potential
 connectivity patterns, and warns from generalizing single-species results
 to the entire community of rocky shore habitats.
description: SeaUrchin_272samples_1122markersTab delimited text file containing general information about 1122 2bRAD SNPs in 272 individuals. The file is organized with a first raw containing headers followed by 1122 rows containing the loci. The first 17 loci are outliers as described in the paper. Headers are: - Catalog ID: locus ID in the Stacks catalogue; - File genepop ID: locus ID in the accompanying genepop file (same as before but with the SNP position embedded in the name); - Consensus sequence: the reference sequence for the locus determined. - Num SNPs: Number of SNPs detected at the locus; - SNPs: position and alleles for all the SNPs detected at the locus; - Num Alleles: total number of alleles for the locus; - Selected SNPs: position used for population analyses; - Alleles in GENEPOP file: correspondence with the alleles in the accompanying genepop file; - 272 columns reporting the genotype for each individuals; missing genotypes are blanks.272samples_1122markers_genepopText file (genepop input format) containing the genotypes used for population genomics analysis. The file contains the genotypes of 1122 SNPs typed in 272 individuals, from 10 population samples. The first 17 loci are outliers as described in the paper. The population order is OTH, KAP, BOK, KOR, TRE, TOG, OTR, POC, FRN, TUN.SNPs_POWSIMText file used as input for POWSIM forward-time simulations with SNPs. The file is based on 8 Adriatic-Ionian populations and 1122 loci. Rename it to POWSIM.IN and use powsim_b to run POWSIM.mt_POWSIMText file used as input for POWSIM forward-time simulations with mtDNA. The file is based on cytochrome b haplotypic frequencies in 7 Adriatic-Ionian populations (Santa Caterina di Nardò, Brindisi, Manfredonia, Lesina, Ancona, Mljet, Miramare), obtained from Maltagliati et al. (2010, Biological Journal of the Linnean Society, 100, 910–923. Rename the file to POWSIM.IN to run POWSIM.