Glacial refugia, postglacial dynamics, and hybrid zones of Pinaceae in Eurasia captured from sedimentary ancient DNA

Boreal forests cover nearly one-third of global forest area. Glacial cycles have shaped the distribution and connectivity of modern Pinaceae genera, yet species-level refugia, postglacial migrations, and hybridization patterns remain unclear due to limited high-resolution taxonomic and temporal data. We applied a hybridization capture approach targeting complete chloroplast genomes of Abies, Larix, Picea, and Pinus to sedimentary ancient DNA (sedaDNA) from 238 samples across 19 sediment records spanning the last 40,000 years from Europe, Asia, and Alaska. Methodological improvements enhanced sequencing depth and genome coverage, enabling detection of low-abundance taxa and the establishment of semiquantitative conifer time series. Population dynamics were inferred from single-nucleotide-polymorphism (SNP)-based species identification, admixture analysis, and haplotype network reconstruction. Previously undocumented glacial refugial Pinaceae populations were identified in western Taymyr, southern Yakutia, and Far East Siberia. Postglacial recolonization began with Larix as a pioneer during the Late Glacial, followed by Picea and Pinus in subsequent warming phases. On the eastern Tibetan Plateau, Picea asperata and Picea purpurea were dominant. Postglacial Pinaceae dynamics across Europe showed early dominance of Pinus sylvestris in high latitude (Kola Peninsula) and Pinus cembra and Pinus mugo in alpine regions (Swiss and Dinaric Alps) from the Late Glacial, later replaced primarily by Picea abies, which dominated in Czechia, southwestern Russia, and possibly southern Sweden, while Pin. sylvestris remained dominant in northern Germany. We also identified undocumented populations, including a potential hybrid spruce, possibly Picea fennica, expanding in the Kola Peninsula during the Early Holocene, and scattered Larix decidua populations across Europe in the Early and Middle Holocene. In the Dinaric Alps, Picea populations shifted from eastern to western lineages during the Younger Dryas–Holocene transition. In south-central Alaska, Picea glauca colonized early and expanded in the Late Holocene. Additionally, we documented potential hybridization zones across Europe between Pic. abies and Picea obovata, Abies sibirica and Abies alba, and L. decidua and Larix sibirica, as well as admixture among Larix species and between Pinus sibirica and Pinus pumila in Siberia. In conclusion, hybridization capture of sedaDNA provided high-resolution insights into past Pinaceae dynamics in Eurasia, supporting future paleogenomic research and forest restoration management.