Tracking ancient admixture and bud phenology using white oak palaeogenomes

Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. In contrast to crops, for trees no ancient genome sequences have been generated so far, despite forests representing the most biologically-rich ecosystems on the planet and trees providing an essential resource for human societies. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3X and 4.0X) and one from France dating to the Bronze Age (1700 BCE, 3.4X). We assessed the underlying species and identified one medieval remain from Lake Constance as a hybrid between Q. robur and Q. petraea and the other two as Q. robur. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.