Chloroplast DNA variation in <i>Epipactis atrorubens</i> populations from northern Greece

<p><i>Epipactis</i> Zinn. is a highly diverse genus, with numerous taxa naturally occurring throughout Europe. While their morphological variability has resulted in contradictory opinions about their taxonomy, the knowledge of the genetic variation of many of its species is limited. Such an example is <i>E. atrorubens</i> in the Balkan Peninsula. In this work, the cpDNA variation of seven <i>E. atrorubens</i> populations from northern Greece and of one population from Germany has been investigated by means of PCR-RFLP markers. Two regions of the cpDNA were studied (<i>trn</i>H-<i>psb</i>A, <i>trn</i>L intron) and four PCR-RFLP markers were employed (<i>trn</i>H-<i>psb</i>A/<i>Hae</i>III, <i>trn</i>H-<i>psb</i>A/<i>Hinf</i>I, <i>trn</i>H-<i>psb</i>A/<i>Vsp</i>I, <i>trn</i>L/<i>Mbo</i>I), which have revealed variation in other <i>Epipactis</i> species. The results demonstrate limited genetic variability in the studied populations, as only one haplotype was present in all the populations (both Greek and German), with the exception of Mt. Menikion (Greece) where a second haplotype was also recorded. This limited variation may be attributed to the properties of the genetic markers involved, to the conserved status of the two cpDNA regions in this species or to factors related to the biology and evolutionary history of <i>E. atrorubens</i>. The presence of a second haplotype only in Mt. Menikion could be attributed to a hybridisation event in the past and/or to the potential existence of a glacial refugium on this mountain.</p

Adaptive and non-adaptive traits in fir populations

<p>The relation between the performance in adaptive traits and the genetic differentiation and variability patterns was examined in fir populations from Greece. In particular, nine fir populations growing in a provenance-test plantation located in central Greece, within the distribution range of the species, were used. The places of origin of the populations cover the range of the fir species distribution in Greece. Four of them represent places where the distribution is continuous and the other five occur in sites of an island-type distribution. The growth and survival rates were measured, and compared to the results taken by analyzing isoenzyme markers, as well as previously published results of morphological traits and terpene markers. Similar patterns of genetic differentiation were obtained by the analysis of isoenzyme markers, terpenes and morphological traits. The results indicated that the genetic differentiation observed is in concordance with the geographical distribution of the studied populations. Genetic diversity in isoenzyme markers as well as growth and survival rates were lower in isolated populations originating from marginal areas. Implications for conservation and breeding are discussed.</p

The core pollen and age data file

The core pollen and age data fil

Complex fine-scale phylogeographic patterns in a putative refugial region of Fagus sylvatica L. (Fagaceae)

<p>This manuscript was accepted for publication at the Botanical Journal of the Linean Society on December 27, 2013.</p> <p>Broad scale chloroplast DNA (cpDNA) studies of beech (<em>Fagus sylvatica</em> L.) populations suggested the existence of glacial refugia and introgression zones in the south-eastern part of Europe. We choose a possible refugium of beech in northern Greece, Mt. Paggeo, which hosts a private cpDNA haplotype for beech, to conduct a fine-scale genetic study. We attempt to confirm or reject the hypothesis of the existence of a small scale refugium and gain understanding of the ecological and topographical factors affecting the spatial distribution of cpDNA haplotypes in the area. Our results reveal a high haplotype diversity in Mt. Paggeo, while the overall distribution of haplotypes show no significant correlation with the ecological characteristics of the beech forests. However, the private haplotype is found in high frequencies in beech forests located within or near ravines having a high spatial overlap with a relict vegetation type, occurring in ecological conditions found mainly within ravines. This result emphasises the importance of topography in the existence of glacial refugia in the wider area. Furthermore, haplotypes originating from two more widespread beech lineages in Greece are found on Mt. Paggeo, indicating a possible mixing of populations originating from a local refugium with populations from different remote refugia that possibly migrated in the area after the last glaciation.</p

trnL sequences and taxonomic assignments Sanger

trnL sequences and taxonomic assignments Sange

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

<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

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

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

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