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Norway spruce (Picea abies (L.) H. Karst.) and Scots pine (Pinus sylvestris L.) are among the most valuable tree species in the Lithuanian forests. Pure stands, which comprise approximately one-quarter of Lithuania’s forest area, provide an important framework for studying tree responses to thinning and susceptibility to species-specific diseases and damage. This study investigated stem health and quality in two experimental Scots pine stands (32 and 39 years old) and four experimental Norway spruce stands (36–43 years old) to assess the influence of the initial stand density and thinning intensity. Each stand consisted of five plots with different initial densities and was subjected to varying thinning regimes from stand establishment. Tree locations were mapped using the pseudolite-based positioning system TerraHärp, and local tree density was calculated. Stem health and damage were assessed using ICP-Forests methodology. Our results showed that across initial densities of 1000–4400 trees ha−1, tree dimensions (diameter and height) were similar, regardless of thinning intensity. The highest levels of stem damage and competition-induced mortality occurred in the densest, unthinned stands, with deer browsing and scraping from fallen trees being the most common damage agents. In contrast, thinned stands exhibited a higher incidence of stem rot (Heterobasidion annosum (Fr.) Bref.), particularly for Norway spruce. Finally, stand density alone did not consistently explain the patterns of tree mortality in either the pine or spruce stands. These findings suggest that cultivating Scots pine and Norway spruce at lower initial densities with minimal thinning may reduce the damage and losses caused by fungal infection. Finally, novel techniques, such as the pseudolite-based positioning system for geolocating trees and drone imaging for assessing tree health, have proven valuable in facilitating field surveys.