The objective of this study was to estimate the effect of pre-commercial tending and commercial thinning on the genetic diversity parameters, especially rare allele loss and diameter–heterozygosity associations, in Scots pine stands by retrospectively modelling the removal of inferior/superior trees. Modelling was based on empirical data of DNA polymorphism in (a) a 60-year-old natural stand and (b) a 20-year-old young stand planted with seeds collected in a seed orchard. Within each of these stands, approximately 400 trees were systematically sampled within 1-ha plots (800 trees in total) and genotyped at 5 neutral and 7 EST-derived nuclear microsatellite markers. There was no significant association between heterozygosity, common allele number and tree diameter in either stand. Even at a high intensity, both simulated tending and commercial thinning had minor effects on the heterozygosity and allelic diversity but caused a significant loss of rare alleles. However, there was a nonlinear relationship between the loss of rare alleles and the thinning intensity in the young stand, such that below 30 % thinning intensity, the rare alleles were lost at a markedly lower rate. In conclusion, the association between commercial value and genetic diversity is weak in Scots pine. Thinning causes loss of rare alleles; however, for specific cases, it could be possible to identify the margins for a slow rate of rare allele loss.

The objective of our study was to test the suitability of several main spatial analysis methods to detect spatial genetic structure in Scots pine stands. We used a sub-set of 47 trees representing a sub-plot of 0.5 ha within a large sample plot selected within a 200-year-old Scots pine stand of natural origin in Punia in central Lithuania. We used 11 nSSR loci to estimate the genetic distance between the 47 trees. The analysis included: PCA, the Mantel test, spatial autocorrelation tests and Bayesian clustering. The results of this pilot study indicate that for well spatially uniform clusters, spatial autocorrelation and Mantel tests may detect the spatial structure, but for highly overlapping structures we suggest Bayesian clustering. Regarding the spatial structure with the subplot of 47 trees selected for this study, 9 highly overlapping clusters were obtained with Bayesian clustering. Our preliminary conclusion is that the spatial genetic structure in natural Scots pine stands is complex and there is an indication of highly intermixed structures, probably a consequence of multiple establishment events.

Most of the former studies on genetic differences between Scots pine populations in Lithuania were based phenotype. The interest is to investigate population differentiation within Lithuania based on neutral highly variable DNA markers such as microsatellites. Objective of the study was to assess genetic differences between 4 Lithuanian populations representing 4 different adaptive environments based on nuclear (nSSR), chloroplast (cpSSR) microsatellites and mitochondrial DNA NAD7.1 locus. The main aim was to pre-screen for the efficiency of a larger number of loci to reveal population differences within Lithuania to be further used on a large material. 7 nSSR loci, 8 cpSSR loci and 1 mtDNA locus were studied in each of the following populations: Labanoras (eastern Lithuania), Juodkrante (western), Visakio Ruda (central) and Mazeikiai (northern). The mtDNA results revealed no marked differences in the frequency of the northern type of mtDNA Nad7.1 295 bp allele with the tendency of slightly higher frequency in the eastern populations. Based on the cpSSR loci, the population differentiation was significant and the among-population variance component was markedly greater than that for the nSSRs. The multilocus clustering based on the cpSSR genetic distance revealed greater similarity between the western Lithuanian populations and genetic separation of central Lithuanian population. Whereas according to the multilocus nSSR clustering, the sea-side spit of Neringa was distinguishing from the rest and the two northern-most populations from Labanoras and Mazeikiai shared a single cluster. In conclusion, our study showed a significant population differentiation especially at the cpSSR loci within Lithuania and provided the background for a more detail investigation based on the loci studied. Merging of present-day regions of provenance are discussed.