Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high-throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long-term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human-induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro-evolutionary response of trees to climate change and human forest management.

To meet the increasing demand of wood biomass worldwide in the context of climate change, developing improved forest tree varieties for high productivity in water-limited conditions is becoming a major issue. This involves breeding for genotypes combining high growth and moderate water loss and thus high water-use efficiency (WUE). The present work provides original data about the genetics of intrinsic WUE (the ratio between net CO2 assimilation rate and stomatal conductance, also estimated by carbon isotope composition of plant material; δ13C) and its relation to growth in Pinus pinaster Ait. First, heritability for δ13C was estimated (0.29) using a 15-year-old progeny trial (Landes provenance), with no significant differences among three sites contrasting in water availability. High intersite correlations (0.63–0.91) and significant but low genotype–environment interactions were detected. Secondly, the genetic architectures of δ13C and growth were studied in a three-generation inbred pedigree, introducing the genetic background of a more-drought-adapted parent (Corsican provenance), at ages of 2 years (greenhouse) and 9 years (plantation). One of the quantitative trait loci (QTLs) identified in the field experiment, explaining 67% of the phenotypic variance, was also found among the QTLs detected in the greenhouse experiment, where it colocalized with QTLs for intrinsic WUE and stomatal conductance. This work was able to show that higher WUE was not genetically linked to less growth, allowing thus genetic improvement of water use. As far as is known, the heritability and QTL effects estimated here are based on the highest number of genotypes measured to date.