We elucidate grapevine evolution and domestication histories with 3525 cultivated and wild accessions worldwide. In the Pleistocene, harsh climate drove the separation of wild grape ecotypes caused by continuous habitat fragmentation. Then, domestication occurred concurrently about 11,000 years ago in Western Asia and the Caucasus to yield table and wine grapevines. The Western Asia domesticates dispersed into Europe with early farmers, introgressed with ancient wild western ecotypes, and subsequently diversified along human migration trails into muscat and unique western wine grape ancestries by the late Neolithic. Analyses of domestication traits also reveal new insights into selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These data demonstrate the role of the grapevines in the early inception of agriculture across Eurasia.

Silver fir (Abies alba Mill.) is a keystone conifer of European montane forest ecosystems that has experienced large fluctuations in population size during during the Quaternary and, more recently, due to land-use change. To forecast the species9 future distribution and survival, it is important to investigate the genetic basis of adaptation to environmental change, notably to extreme events. For this purpose, we here provide a first draft genome assembly and annotation of the silver fir genome, established through a community-based initiative. DNA obtained from haploid megagametophyte and diploid needle tissue was used to construct and sequence Illumina paired-end and mate-pair libraries, respectively, to high depth. The assembled A. alba genome sequence accounted for over 37 million scaffolds corresponding to 18.16 Gb, with a scaffold N50 of 14,051 bp. Despite the fragmented nature of the assembly, a total of 50,757 full-length genes were functionally annotated in the nuclear genome. The chloroplast genome was also assembled into a single scaffold (120,908 bp) that shows a high collinearity with both the A. koreana and A. sibirica complete chloroplast genomes. This first genome assembly of silver fir is an important genomic resource that is now publicly available in support of a new generation of research. By genome-enabling this important conifer, this resource will open the gate for new research and more precise genetic monitoring of European silver fir forests.

Aim: Knowing a species' response to historical climate shifts helps understanding its perspectives under global warming. We infer the hitherto unresolved postglacial history of Pinus cembra. Using independent evidence from genetic structure and demographic inference of extant populations, and from palaeoecological findings, we derive putative refugia and re‐colonisation routes.Location: European Alps and Carpathians.Taxa: Pinus cembra. Methods: We genotyped nuclear and chloroplast microsatellite markers in nearly 3000 individuals from 147 locations across the entire natural range of P. cembra. Spatial genetic structure (Bayesian modelling) and demographic history (approximate Bayesian computation) were combined with palaeobotanical records (pollen, macrofossils) to infer putative refugial areas during the Last Glacial Maximum (LGM) and re‐colonisation of the current range.Results: We found distinct spatial genetic structure, despite low genetic differentiation even between the two disjunct mountain ranges. Nuclear markers revealed five genetic clusters aligned East–West across the range, while chloroplast haplotype distribution suggested nine clusters. Spatially congruent separation at both marker types highlighted two main genetic lineages in the East and West of the range. Demographic inference supported early separation of these lineages dating back to a previous interstadial or interglacial c. 210,000 years ago. Differentiation into five biologically meaningful genetic clusters likely established during postglacial re‐colonisation.Main Conclusions: Combining genetic and palaeoecological evidence suggests that P. cembra primarily survived the LGM in ‘cold period’ refugia south of the Central European Alps and near the Carpathians, from where it expanded during the Late Glacial into its current Holocene ‘warm period’ refugia. This colonisation history has led to the distinct East–West structure of five genetic clusters. The two main genetic lineages likely derived from ancient divergence during an interglacial or interstadial. The respective contact zone (Brenner line) matches a main biogeographical break in the European Alps also found in herbaceous alpine plant species.

Variation in genetic diversity across species ranges has long been recognized as highly informative for assessing populations’ resilience and adaptive potential. The spatial distribution of genetic diversity within populations, referred to as fine‐scale spatial genetic structure (FSGS), also carries information about recent demographic changes, yet it has rarely been connected to range scale processes. We studied eight silver fir (Abies albaMill.)population pairs (sites), growing at high and low elevations, representative of the main genetic lineages of the species. A total of 1,368 adult trees and 540 seedlings were genotyped using 137 and 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a clear east‐west isolation‐by‐distance pattern consistent with the post‐glacial colonization history of the species. Genetic differentiation among sites (F_CT= 0.148) was an order of magnitude greater than between elevations within sites (F_SC= 0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modelling revealed that elevation and, to a lesser extent, post‐glacial colonization history, but not climatic and habitat variables, were the best predictors of FSGS across populations. These results suggest that high elevation habitats have been colonized more recently across the species range. Additionally, paternity analysis revealed a high reproductive skew among adults and a stronger FSGS in seedlings than in adults, suggesting that FSGS may conserve the signature of demographic changes for several generations. Our results emphasize that spatial patterns of genetic diversity within populations provide information about demographic history complementary to non‐spatial statistics, and could be used for genetic diversity monitoring, especially in forest trees.