Sampling locations for Bonga shad.

<p>MAU: Etoile Bay, Mauritania; SEN: St Louis, Senegal; SAL : Foundiougne, Saloum, Senegal ; GAM : Tendaba, The Gambia ; CAS : Diogue, Casamance, Senegal ; GUI : Conakry, Guinea ; ICA : Aby, Côte d’Ivoire; CON: Loango Bay, Congo; ANG: Luanda, Angola. Grey areas represent estuarine conditions according to Charles-Dominique and Albaret [34]. Red dots indicate scientific sampling stations where Bonga shad were identified.</p

Genetic differentiation in Bonga shad along West African shoreline recovered with 7 EPIC loci.

<p>Admixture proportions at each sampling location (black dots) of the 4 genetic clusters recovered by TESS are shown in pies-charts. Gene flow barriers are highlighted using the spatial autocorrelation method, Barrier 2.2. are indicated by violet bars on the map, and their reliability was estimated using a bootstrap procedure on seven <i>F</i>_ST matrices (one per nuclear locus). Line thickness of gene flow barriers is proportional to the bootstrap value and green numbers indicate the number of loci that report significant genetic heterogeneity (i.e. number of loci supporting a genetic break).</p

Sparus_aurata_genotypes_data_files

This ZIP archive contains 3 data files (as described in Table 1), "3_CANDIDATE_SSR_10_pops.gtx" is the GENETIX input file matrix for the 3 candidate genes SSRs genotyped in 10 locations, "7_ANONYMOUS_3_CANDIDATE_SSR_5_pops.gtx" is the GENETIX input file matrix for the 7 anonymous SSRs and 3 candidate genes SSRs genotyped in 5 locations, and "Sparus_44loci_AFLPSURV.txt" is the AFLPSURV input file table for the 44 AFLP markers in 10 locations

SNP genotypes

SNP genotype

Microsatellite genotypes

Microsatellite genotype

Primers used for PCR-amplification of the Tmo-4C4 nuclear locus and the cytochrome <i>b</i> and cytochrome <i>c</i> oxidase I genes.

<p>Primers used for PCR-amplification of the Tmo-4C4 nuclear locus and the cytochrome <i>b</i> and cytochrome <i>c</i> oxidase I genes.</p

Maximum likelihood tree reconstructed from the <i>Apistogramma</i> concatenated haplotype dataset of the mitochondrial cytochrome <i>b</i> and cytochrome <i>c</i> oxydase I genes and the Tmo-4C4 nuclear locus.

<p>Haplotypes are detailed in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182618#pone.0182618.s006" target="_blank">S2 Table</a>. Numbers at nodes are for bootstrap percentages (≥ 50%) and posterior probabilities (≥ 0.85). Black circles indicate nodes with BP = 100% and PP = 1.00, while grey circles are for nodes with a weak support (BP < 50% and PP < 0.85). Nodes with “-”are weakly supported in maximum likelihood approach or Bayesian inference. Branches with “*” indicate short internal branches not significantly different from zero.</p