Within-site outlier detection.

<p>Results of FDIST and SBM within each <i>A</i>. <i>alba</i> and <i>A</i>. <i>cephalonica</i> study sites. It is noteworthy that some outliers were detected in two study sites.</p

Hierarchical (multi-site) outlier detection.

<p>Result of HBM (hierarchical Bayesian approach) on the complete <i>A</i>. <i>alba</i> dataset. <i>θ</i>_{<i>Elev(m)</i>} are locus-specific effects on genetic differentiation among populations belonging to different elevations. On the left, the estimated values of <i>θ</i>_{<i>Elev(m)</i>} with their 95% posterior credible intervals. The markers are sorted by decreasing values of <i>θ</i>_{<i>Elev(m)</i>} and the dotted lines represent the inter-quantile limits [Q₁-1.5(Q₃-Q₁); Q₃+1.5(Q₃-Q₁)]. On the right, the distribution of <i>θ</i>_{<i>Elev(m)</i>} and the fitted normal distribution. The arrow indicates the two loci detected below the neutral background in the complete dataset under a 1% probability threshold.</p

Consistent outliers detected twice above the neutral background (by two different approaches).

<p>The first column describes the SNP number, the second column the SNP ID. The third column describes the study site in which the outliers were detected and the method used: FDIST (within-site coalescent method) and SBM under a 1% threshold (within-site Bayesian method). Study sites IDs are described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158216#pone.0158216.t001" target="_blank">Table 1</a>. The complete list of outliers detected, all methods confounded, is provided in S1 Table.</p

Genetic structure.

<p>Location of the study sites (<i>A</i>. <i>alba</i>, sites 1 to 9 and <i>A</i>. <i>cephalonica</i>, site 10) and genetic structure of <i>A</i>. <i>alba</i> populations revealed by STRUCTURE for <i>K</i> = 2 (top) and <i>K</i> = 4 (bottom). The map was created in ArcMap v.9.3 (ESRI. Redlands, CA). The European basemap is copyrighted by EUROSTATS (EuroGeographics for the administrative boundaries) and is available at: <a href="http://ec.europa.eu/eurostat/web/gisco/geodata/reference-data/administrative-units-statistical-units" target="_blank">http://ec.europa.eu/eurostat/web/gisco/geodata/reference-data/administrative-units-statistical-units</a>. The black area shows the distribution range of <i>A</i>. <i>alba</i> (according to EUFORGEN 2009, <a href="http://www.euforgen.org/" target="_blank">http://www.euforgen.org</a>). Study sites IDs are described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158216#pone.0158216.t001" target="_blank">Table 1</a>.</p

Idiosyncrasy between sites.

<p>Observed genotypic frequencies in the different sites at SNP 255 (genotypes CC, CT and TT). SNP 255 was detected by two within-site outlier detection methods (FDIST and SBM) in site 9 (purple line), but in no other site. In addition, significant GEAs were detected in site 9 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158216#pone.0158216.s015" target="_blank">S2 Table</a>).</p

Power of the Bayesian approaches (HBM, SBM and BAYESCAN) to detect outliers for selection from simulated data.

<p>False-discovery rates (<i>FDR</i>) and false non-discovery rates (<i>FNR</i>) were empirically assessed under different scenarios of divergent and/or homogenizing selection, by varying the proportion of selected loci, and selection strength.</p

<i>A</i>. <i>alba</i> and <i>A</i>. <i>cephalonica</i> study sites and sampling design.

<p><i>A</i>. <i>alba</i> and <i>A</i>. <i>cephalonica</i> study sites and sampling design.</p