In the course of the 4th German National Forest Inventory, samples of the two oak species Quercus robur and Quercus petraea were collected throughout Germany. Genetic analyses were performed based on 403 nuclear, 21 chloroplast and 7 mitochondrial markers. The analyses showed good differentiation between the two species based on genetic data. Both species are connected through hybridization and introgression, but only about 2% of the samples analysed were found to be potential first-generation hybrids. Identical chloroplast and mitochondrial haplotypes with lineage specific distribution patterns were identified in both species. Different haplo- and mitotypes showed a tight linkage. Analysis of nuclear SNPs revealed a clear genetic structure in Q. robur, which appears to be largely of natural origin and can be explained by the postglacial recolonization routes through which the species dispersed throughout Germany after the last glacial maximum. Environmental influences, most importantly continentality, also appear to have an impact on the genetic structure of Q. robur, possibly caused by preadaptation within the refugial source-populations. For Q. petraea, the situation seems more complicated and no clear genetic structure could be identified.
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