Chloroplast and nuclear genetic diversity and differentiation across European taxa of white oaks (Quercus L. section Quercus)

An extensive analysis on the chloroplast and nuclear genetic diversity and differentiation across European taxa of white oaks (Quercus L. section Quercus) was performed. Chloroplast DNA (cpDNA) variation was studied to clarify the biogeography and the history of the populations and to reconstruct genealogical relations between cpDNA haplotypes. Furthermore, a nuclear SSRs analysis was performed to provide data on the genetic structure and diversity and to verify if the groups of oaks analysed were genetically distinct and if their identification was in accordance with the current taxonomic classification. The study was carried out over a vast area of the central and southern Europe, the Balkan Peninsula, and the northern Africa. The sampling design included 11 countries and 1987 individuals (trees) belonging to 93 populations and representing 13 taxa of the Quercus genus. The genomic DNA of 270 samples was analysed by means of DNA sequence polymorphism at two plastid loci: the trnH-psbA intergenic spacer and a portion of the trnK-matK region. Haplotype diversity, pairwise uncorrected p-genetic distances, number of polymorphic sites, nucleotide polymorphism, nucleotide diversity, and number of parsimony informative characters in the two marker regions were evaluated. Moreover, genealogical relations between cpDNA haplotypes were reconstructed. The nuclear microsatellite markers analysis was performed on a subset of 1072 individuals belonging to 58 populations. The patterns of the genetic structure and the hierarchical structure of the sampled populations were assessed. In addition, genetic diversity and differentiation within and among populations were estimated and analysis of molecular variance (AMOVA) and Principal Coordinates Analysis (PCoA) were performed. The phylogeographic analysis based on the study of the chloroplast DNA variation allowed to confirm the relatively recent colonization of the section Quercus in Eurasia and to document the little differentiated plastome of this oaks group, as shown by the low degree of diversity found in the fourteen haplotypes identified in the studied area. While the detected nucleome variability did not reflect the considerable morphological variability responsible for the many ecomorphotypes and the taxonomic confusion in the European white oaks group. Based on the obtained results, five genetically distinct groups, among the twelve taxa identified based on morphological features, were recognized, so the taxonomic classification for the European white oaks was not always confirmed by molecular analyses. This study demonstrated that both the young history of the European white oaks and the repeated events of hybridisation and introgression are responsible for a group that is not still genetically fixed and resolved.