  Genetic analysis was carried out in order to provide insights into
differentiation among populations of two interfertile oak species, Quercus
petraea and Quercus robur. Gene flow between the two species, local adaptations
and speciation processes in general, may leave differential molecular
signatures across the genome. Three interspecific pairs of natural populations
from three ecologically different regions, one in central Europe (SW Germany)
and two in the Balkan Peninsula (Greece and Bulgaria) were sampled. Grouping of
highly informative SSR loci was made according to the component of variation
they express - interspecific or provenance specific. Species and provenance
discriminant loci were characterized based on FSTs. Locus specific FSTs were
tested for deviation from the neutral expectation both within and between
species. Data were then treated separately in a Bayesian analysis of genetic
structure. By using three species discriminant loci, high membership
probability to inferred species groups was achieved. On the other hand,
analysis of genetic structure based on five provenance discriminant loci was
correlated with geographic region and revealed shared genetic variation between
neighbouring Q. petraea and Q. robur. Small sets of highly variable nuclear
SSRs were sufficient to discriminate, either between species or between
provenances. Thus, an effective tool is provided for molecular identification
of both species and provenances. Furthermore, data suggest that a combination
of gene flow and natural selection forms these diversity patterns. Species
discriminant loci might represent genome regions affected by directional
selection, which maintains species identity. Provenance specific loci might
represent genome regions with high interspecific gene flow and common adaptive
patterns to local environmental factors.
