Genetic variation of <i>Abies cilicica</i> and other Mediterranean <i>Abies</i> species.

<p>Pie charts are used to depict the gene diversity corrected for sample size <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Nei1" target="_blank">[55]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Hartl1" target="_blank">[56]</a> and the rarefied allelic richness <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Hurlbert1" target="_blank">[57]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-ElMousadik1" target="_blank">[58]</a>, averaged over 10 nuclear microsatellite loci, for <i>A. cilicica</i> in Lebanon (CILI), <i>A. bornmuelleriana</i> in Turkey (BORN), <i>A. cephalonica</i> in Greece (CEPH), <i>A. alba</i> in the French Southern Alps (ALBA1), <i>A. alba</i> in the French Pyrenees (ALBA2), and <i>A. marocana</i> in Morocco (MARO). Diameter of pie charts is relative to the correspondent rarefied allelic richness of the species. Proportion of red or blue color within pie charts is relative to the correspondent gene diversity of the species. Blue and red colors are employed to separate the studied fir populations into a group with significant lower genetic variation (red pie charts), and a group with significant higher genetic variation (blue pie charts) based on 10000 permutations of populations among groups performed in fstat version 2.9.3.2 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Goudet1" target="_blank">[54]</a>.</p

Genetic variation, population structure and phylogeography in the Northeastern and Southwestern ridges.

<p><i>H_O</i> observed heterozygosity per deme <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Nei2" target="_blank">[76]</a>; <i>H_E</i> expected heterozygosity per deme and corrected for sample size <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Nei2" target="_blank">[76]</a>; <i>A_R</i> rarefied allelic richness per deme for a sample size of 102 gene copies <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Hurlbert1" target="_blank">[57]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-ElMousadik1" target="_blank">[58]</a>; <i>H_T</i> overall gene diversity per deme <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Nei2" target="_blank">[76]</a>; <i>F_IS</i> inbreeding coefficient per deme <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Weir2" target="_blank">[59]</a>; <i>F_ST</i> genetic differentiation per deme based on allele identity <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Weir2" target="_blank">[59]</a>; <i>R_ST</i> genetic differentiation per deme based on allele size <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Slatkin3" target="_blank">[63]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Michalakis1" target="_blank">[64]</a>; <i>pR_ST</i> permuted <i>R_ST</i> after allele size permutation test <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Hardy2" target="_blank">[65]</a>. Columns 1 to 6 indicate the statistical differences in genetic variation and population structure between populations of the Northeastern ridge and populations of the Southwestern ridge. Columns 7 and 8 indicate the results of the test of phylogeographic patterns corresponding to the statistical differences between <i>R_ST</i> and <i>pR_ST</i> within the Northeastern ridge and within the Southwestern ridge. * P<0.05; ** P<0.01; *** P<0.001. ^NSNon-Significant test.</p

Asymmetric Northeast-Southwest migration of <i>Abies cilicica</i> in Lebanon.

<p>The Northeastern and Southwestern ridges correspond to the two genetically-distinct demes assigned by baps <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Corander1" target="_blank">[71]</a>. Populations of the Northeastern ridge are plotted in green color while those of the Southwestern ridge are plotted in magenta color. A likelihood-based Bayesian assignment test <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Rannala1" target="_blank">[79]</a> performed in geneclass2 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Piry1" target="_blank">[77]</a> allowed the detection, in the Southwestern ridge, of 3 F₀ migrants originating from the Northeastern ridge. It has also allowed the detection, in the Northeastern ridge, of 1 F₀ migrant originating from the Southwestern ridge, suggesting an asymmetric Northeast-Southwest migration.</p

Genetic variation and genetic distinctiveness of <i>Abies cilicica</i> and other Mediterranean <i>Abies</i> species.

<p><i>H_O</i> observed heterozygosity per population averaged over loci; <i>H_E</i> expected heterozygosity corrected for sample size averaged over loci <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Nei1" target="_blank">[55]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Hartl1" target="_blank">[56]</a>; <i>A_{R (20)}</i> rarefied allelic richness for a sample size of 20 gene copies averaged over loci <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Hurlbert1" target="_blank">[57]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-ElMousadik1" target="_blank">[58]</a>; <i>A_{R (6)}</i> rarefied allelic richness for a sample size of 6 gene copies averaged over loci <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Hurlbert1" target="_blank">[57]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-ElMousadik1" target="_blank">[58]</a>; <i>П_s</i> rarefied private allelic richness for a sample size of 20 gene copies averaged over loci <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Hurlbert1" target="_blank">[57]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Kalinowski1" target="_blank">[60]</a>; <i>F_IS</i> inbreeding coefficient <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Weir2" target="_blank">[59]</a>. MARO refers to <i>Abies marocana</i> in Morocco, BORN to <i>Abies bornmuelleriana</i> in Turkey, CEPH to <i>Abies cephalonica</i> in Greece, ALBA1 to <i>Abies alba</i> in the French Southern Alps and ALBA2 to <i>Abies alba</i> in the French Pyrenees. Other codes refer to <i>Abies cilicica</i> in Lebanon (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone-0090086-t001" target="_blank">Tables 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086.s001" target="_blank">S1</a>).</p

Range of distribution of <i>Abies cilicica</i> in the Eastern Mediterranean.

<p>Remnant populations of <i>Abies cilicica</i> in Turkey, Syria and Lebanon are plotted in red onto the map of the Eastern Mediterranean. Remnant populations of <i>Abies cilicica</i> in Lebanon are plotted in green onto the map of Lebanon where they are currently found on the western slopes of the northern part of Mount Lebanon. Geographical position of <i>Abies cilicica</i> in Turkey and Syria were plotted from a euforgen map <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Alizoti1" target="_blank">[105]</a> while the geographical position of <i>Abies cilicica</i> in Lebanon corresponds to our sampling data. Map was prepared using qgis version 1.8.0 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-QGIS1" target="_blank">[106]</a> and the gmt package <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Wessel1" target="_blank">[107]</a> within r <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-R1" target="_blank">[108]</a>.</p

DATA : Abies data

<p>BlastX and  functional annotation (sheet 1), SNPs design (sheet 2) and SNPs Genotyping* (sheet 3).</p> <p>*<em>Abies alba</em> and<em> A. cephalonica</em> populations (10 altitudinal gradients accross Europe from French Pyrennées to Greece) / 273 SNPs</p

Isolation-by-distance and non-equilibrium conditions between dispersal and genetic drift.

<p>The logarithm of genetic similarity is plotted against the logarithm of geographic distance among population pairs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Slatkin2" target="_blank">[26]</a>. Estimations of slope, intercept and R² of the relationships were calculated using Reduced Major Axis (RMA) regression <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Hellberg1" target="_blank">[83]</a>. The RMA regression explained only 5% of the variance in the whole distribution area of <i>Abies cilicica</i> in Lebanon. Analysis was performed in ibdws <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Jensen1" target="_blank">[81]</a>.</p

Allele frequency distribution over different allele frequency classes for each population of <i>Abies cilicica</i>.

<p>This figure shows the distribution of allele frequencies across the 15 local populations. The values were obtained using the mode-shift test <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Luikart2" target="_blank">[89]</a>. The distribution of allele frequencies across the 15 local populations is plotted using different colors. All populations showed a higher abundance of rare alleles (frequency<0.1) than alleles at intermediate frequencies (0.1–0.2).</p

Origin, location and sample size of <i>Abies cilicica</i> populations in Lebanon.

<p>*Elevation in meters above sea level.</p>1<p>membership of the local population to deme 1 (Northeastern ridge).</p>2<p>membership of the local population to deme 2 (Southwestern ridge).</p

Observed and simulated values of the modified Garza-Williamson index for <i>Abies cilicica</i> populations.

<p>This figure shows the different observed values of the <i>M</i>-ratios calculated for the microsatellite loci and the values of the simulated critical <i>M</i> threshold (<i>M</i>_c) below which a bottleneck is evident. The observed <i>M</i>-ratio values are displayed in black solid line. The <i>M</i>_c values calculated for <i>θ</i> = 10, <i>θ</i> = 1, <i>θ</i> = 0.5, and <i>θ</i> = 0.1 are respectively displayed in red, blue, green and orange solid lines. All the observed <i>M</i>-ratio values were significantly higher than the simulated <i>M</i>_c values for different pre-bottleneck <i>θ</i> values. Values of the <i>M</i>-ratio and the <i>M</i>_c parameters were obtained using m-p-val and critical_m <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090086#pone.0090086-Garza1" target="_blank">[84]</a>.</p