Human impact on tree species occurs directly through population transfer, regeneration, and the silvicultural regimes applied, and this impact is large as it lasts for centuries [30,31]. However, it will be many years before tree-breeding programmes for all important tropical and north temperate tree species will result in the conservation of gene resources in clone banks and seed orchards, and in the production of commercial quantities of seed of the correct provenance [32]. In the meantime, the elimination of the world’s remaining natural forest ecosystems continues, and evolutionary centres, sources of great genetic variability and new forms of plant life, are being massively disrupted or destroyed [33]. Wood harvesting has a direct impact on the genetic diversity of tree populations through changes in population size (effective population size), age and size distribution, density, spatial distribution of trees and genotypes, etc. Non-commercial forest species are also affected by logging, as it causes alterations in environmental conditions for animals and plants [34]. In order to fully understand how management systems affect the sustainable use of forests and their conservation in the long term, forest genetic monitoring (FGM) can serve as an appropriate tool [10]. Konnert et al. [35] confirmed the necessity and urgency for developing an FGM system, as problems in the genetic processes of tree populations are usually not immediately observable (e.g., Piotti et al. [36], Hoban et al. [37]) by measuring the natural regeneration or vitality of seeds. However, for an effective genetic monitoring programme with respect to the detection of management impact, it is first necessary to assess the baseline data, i.e., the random fluctuations of the genetic structure of natural populations, in order to be able to detect genetic changes caused by anthropogenic factors later on [38].

2. Genetic Processes of Tree Populations

The traits of hemiboreal trees’ life history are a manifestation of species patterns and processes recurring over the scales of species distributions [41,42]. The variety of the life history of a species and how it interacts in the community is a manifestation of a genetic code written in the genomes of species, which exist for time intervals of the order of several million years—the average lifespan of a species [42]. Whenever the environment deviates from the optimum, genotypic fitness of a species ensures that biotic processes can compensate for disadvantageous changes [48]. The fitness of a genotype refers to the average contribution that carriers of that genotype make to the gene pool of successive generations [52]. The past interaction of evolutionary factors—mutation, genetic drift, natural selection, gene flow, and phenotypic plasticity—is responsible for the standing population’s genetic structure and variation both within and between species [30]. Population adaptedness of successive generations describes the ability of a species to live, adapt and reproduce in a wide variety of reproductive environments [52,53]. Mutation is the engine of evolution in that it generates the genetic variation on which natural selection acts, therefore the inclusion of genetic information from multiple species is critical because even functionally similar species can be characterized by very different evolutionary histories and contemporary genetic patterns that can play a major role in providing resilience to future change [49,50].

Long-lived trees as the foundation species of forest ecosystems provide a matrix of resources and habitats for associated organisms, with interactions ranging from beneficial to detrimental [51]. Length of reproductive age and a long-lasting ability to reproduce sexually or vegetatively help tree species to maintain their genetic structure unchanged after founder population establishment, unless human activity is intensive [30]. Reproductive cycles of forest tree species last two, three years or more, seed productivity varies from year to year, and mast years come irregularly. Thus, depending on the biology of the species, the applied forest management and other factors, it might take from several years to several decades before a new generation of forest trees is effectively established [91]. Reproductive environments of species could be considered as a factor increasing the adaptedness of species, especially under marginal conditions [54]. For instance, if a newly established population is small and has no further contact with leading edge/main distribution (no gene flow), then it can suffer due to low genetic variation, which might lead to genetic drift, high inbreeding, and decline [55–57]. Depending on human activity, e.g., assisted migration, can improve the level of genetic diversity, e.g., through artificial or supplementary planting [58–60].

Among the three main indicators of FGM (natural selection, genetic variation, and gene flow/mating system), natural selection is one of the most important evolutionary factors that can directly affect and change the allele frequencies of even a small forest population/cohort over a short time and can increase the rate of adaptation to environmental conditions [64]. It is based on the assessment of several verifiers through field observations of seasonal phenomena, such as the abundance and synchrony of flowering, the periodicity and intensity of fructification, the abundance of natural regeneration, etc. In most plant species, the timing of seasonal events—regenerative and reproductive phenophases—can be very sensitive to climate and environmental changes, making phenology one of the most variable characteristics of plants [7,8,72,73]. Nonetheless, the genetic monitoring of community phenology, in order to obtain characteristic plant cycles as well as their responses to seasonal and climatic changes, is a promising tool for conservation and management of genetic conservation units (GCUs).