Variation in the lengths of restriction fragments (RFLPs) of the whole chloroplast DNA molecule was studied in 174 populations of Quercus ilex L. sampled over the entire distribution of this evergreen and mainly Mediterranean oak species. By using five endonucleases, 323 distinct fragments were obtained. From the 29 and 17 cpDNA changes identified as site and length mutations, respectively, 25 distinct chlorotypes were distinguished, mapped and treated cladistically with a parsimony analysis, using as an outgroup Q. alnifolia Poech, a closely related evergreen oak species endemic to Cyprus where Q. ilex does not grow. The predominant role of Q. ilex as maternal parent in hybridization with other species was reflected by the occurrence of a single very specific lineage of related chlorotypes, the most ancestral and recent ones being located in the southeastern and in the northwestern parts of the species' geographical distribution, respectively. The lineage was constituted of two clusters of chlorotypes observed in the 'ilex' morphotyped populations of the Balkan and Italian Peninsulas (including the contiguous French Riviera), respectively. A third cluster was divided into two subclusters identified in the 'rotundifolia' morphotyped populations of North Africa, and of Iberia and the adjacent French regions, respectively. Postglacial colonization probably started from three distinct southerly refugia located in each of the three European peninsulas, and a contact area between the Italian and the Iberian migration routes was identified in the Rhône valley (France). Chlorotypes identical or related to those of the Iberian cluster were identified in the populations from Catalonia and the French Languedoc region, which showed intermediate morphotypes, and in the French Atlantic populations which possessed the 'ilex' morphotype, suggesting the occurrence of adaptive morphological changes in the northern part of the species' distribution.

The results support a Middle-Eastern or a central Mediterranean origin for cork oak with subsequent westward colonization during the Tertiary Period, and suggest that the 'ilex' chlorotype variation does not reflect entirely cytoplasmic introgression by Q. ilex but originated partly in Q. suber.

Summary• Among oak species, Quercus ilex is classified as a monoterpene emitter and Q. suber is mainly known as a nonisoprenoid emitter. The extent and origin of this diversification is unknown.• We examined intra-and interspecific emission variability in two mixed stands which differed in their level of hybridization and reciprocal genetic introgression based on variations in cytoplasmic (chloroplast DNA) and nuclear (allozyme) markers.• At both sites all trees identified as Q. ilex , or as recent descendants from Q. ilex × Q. suber hybrids, emitted monoterpenes. Of Q. suber trees (genetically introgressed or not by Q. ilex ), 91% were also monoterpene emitters, and the remainder nonemitters. One tree identified as a Q. canariensis × Q. ilex hybrid emitted both isoprene and monoterpenes. Compared with Q. ilex , the standard emission rate of Q. suber was higher in summer and lower in autumn. Both species emitted the same monoterpenes, proportions of which showed significant intra-and interspecific variability.• The results suggest that Q. suber populations in the French Mediterranean intrinsically emit monoterpenes, and that gene flow between oak species contributes to diversification of emission signatures.