It is commonly believed that trees were absent in Scandinavia during the last glaciation and first recolonized the Scandinavian Peninsula with the retreat of its ice sheet some 9000 years ago. Here, we show the presence of a rare mitochondrial DNA haplotype of spruce that appears unique to Scandinavia and with its highest frequency to the west-an area believed to sustain ice-free refugia during most of the last ice age. We further show the survival of DNA from this haplotype in lake sediments and pollen of Trøndelag in central Norway dating back ~10,300 years and chloroplast DNA of pine and spruce in lake sediments adjacent to the ice-free Andøya refugium in northwestern Norway as early as ~22,000 and 17,700 years ago, respectively. Our findings imply that conifer trees survived in ice-free refugia of Scandinavia during the last glaciation, challenging current views on survival and spread of trees as a response to climate changes.

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios.

Norway spruce (Picea abies [L.] Karst.) is a broadly distributed European conifer tree whose history has been intensively studied by means of fossil records to infer the location of full-glacial refugia and the main routes of postglacial colonization. Here we use recently compiled fossil pollen data as a template to examine how past demographic events have influenced the species' modern genetic diversity. Variation was assessed in the mitochondrial nad1 gene containing two minisatellite regions. Among the 369 populations (4876 trees) assayed, 28 mitochondrial variants were identified. The patterns of population subdivision superimposed on interpolated fossil pollen distributions indicate that survival in separate refugia and postglacial colonization has led to significant structuring of genetic variation in the southern range of the species. The populations in the northern range, on the other hand, showed a shallow genetic structure consistent with the fossil pollen data, suggesting that the vast northern range was colonized from a single refugium. Although the genetic diversity decreased away from the putative refugia, there were large differences between different colonization routes. In the Alps, the diversity decreased over short distances, probably as a result of population bottlenecks caused by the presence of competing tree species. In northern Europe, the diversity was maintained across large areas, corroborating fossil pollen data in suggesting that colonization took place at high population densities. The genetic diversity increased north of the Carpathians, probably as a result of admixture of expanding populations from two separate refugia.

Norway spruce of northern Europe expanded at the end of the last glacial out of one refugium in Russia. To provide a detailed insight into how the genetic structure in the northern European lineage of this species has been shaped by postglacial migration, recurrent pollen flow and marginality, we here compare variation at seven highly variable nuclear microsatellite loci in 37 populations (1715 trees) with mitochondrial DNA variation. Microsatellite diversity was high (H E ¼ 0.640) and genetic differentiation was low (F ST ¼ 0.029). The microsatellite structure supported a mitochondrial DNA (mtDNA)-based hypothesis of two migration routes out of a single Russian refugium; one northwestern over Finland to northern Scandinavia, and one southwestern across the Baltic Sea into southern Scandinavia. Microsatellite diversity was maintained along the southwestern migration routes, whereas a significant decrease was observed towards the north. In contrast, the mtDNA diversity suggested higher amounts of historical gene flow towards the north than along the southwestern migration route. This suggests that the loss of nuclear diversity after postglacial colonization has been efficiently replenished by pollen-mediated gene flow in the south. Towards the north, smaller effective population size because of more limited seed and pollen production may have caused decreased nuclear diversity and increased inbreeding, reflecting the ecological marginality of the species in the north.

Boreal species were repeatedly exposed to ice ages and went through cycles of contraction and expansion while sister species alternated periods of contact and isolation. The resulting genetic structure is consequently complex, and demographic inferences are intrinsically challenging. The range of Norway spruce (Picea abies) and Siberian spruce (Picea obovata) covers most of northern Eurasia; yet their geographical limits and histories remain poorly understood. To delineate the hybrid zone between the two species and reconstruct their joint demographic history, we analysed variation at nuclear SSR and mitochondrial DNA in 102 and 88 populations, respectively. The dynamics of the hybrid zone was analysed with approximate Bayesian computation (ABC) followed by posterior predictive structure plot reconstruction and the presence of barriers across the range tested with estimated effective migration surfaces. To estimate the divergence time between the two species, nuclear sequences from two well-separated populations of each species were analysed with ABC. Two main barriers divide the range of the two species: one corresponds to the hybrid zone between them, and the other separates the southern and northern domains of Norway spruce. The hybrid zone is centred on the Urals, but the genetic impact of Siberian spruce extends further west. The joint distribution of mitochondrial and nuclear variation indicates an introgression of mitochondrial DNA from Norway spruce into Siberian spruce. Overall, our data reveal a demographic history where the two species interacted frequently and where migrants originating from the Urals and the West Siberian Plain recolonized northern Russia and Scandinavia using scattered refugial populations of Norway spruce as stepping stones towards the west.