The largest populations of veteran oak trees in Europe are found in British parklands: managed wood pastures up to 1000 years old. Here, we present genomic evidence that parkland oak populations harbour considerable diversity and grew from local seed sources. We found some evidence for natural regeneration of offspring and for hybridization between pedunculate and sessile oak. We detected signatures of past gene flow between these two species and few regions of high differentiation within their genomes. Future expansion of this dataset may allow us to test for a genomic basis of acute oak decline, a syndrome of particular concern in parkland environments. Summary• The two predominant oak species in Europe, Quercus robur (English or pedunculate oak) and Quercus petraea (sessile oak), have a long history of human intervention.In Britain, a common management regime is parklands, often surrounding country houses. Little is known about how seeds were sourced for parkland oak populations nor the genetic diversity that they contain.• We sequenced the whole genomes of 386 trees from four British parkland sites to characterize the nuclear and chloroplast genetic structure and diversity of oak parkland populations. We assembled the chloroplast genomes and matched these to restriction enzyme fragment chloroplast haplotypes found in previous studies of ancient woodlands.• We found over two million high-quality nuclear single-nucleotide polymorphisms (SNPs), allowing us to identify 360 Q. robur, 10 Q. petraea and 16 hybrid individuals with confidence. We identified 81 coding regions exhibiting strong differentiation between the two species. We found evidence for selective sweeps in Q. robur near some regions containing genes with putative involvement in stress tolerance.• We detected a few very close relatives within some sites, suggesting natural regeneration or local seed planting. There was little differentiation among the Q. robur populations at the four sites. Chloroplast genomes found in each parkland

Acute Oak Decline (AOD) is complex syndrome affecting Britain’s keystone native oak species, (Quercus robur L. and Q. petraea L. (Matt.) Liebl.), in some cases causing mortality within five years of symptom development. The most distinguishable symptom is weeping stem lesions, from which four species of bacteria have been isolated: Brenneria goodwinii, Gibbsiella quercinecans, Lonsdalea britannica and Rahnella victoriana. We do not yet know where else these bacteria exist, and little is known about the relationship of the wider oak leaf microbiome (phyllosphere) to acute oak decline. Here we investigate whether incidental evidence from a large oak genome re-sequencing dataset could be used to detect these bacteria in oak foliage, and whether bacterial incidence co-varied with AOD status or location. Oak leaves and buds were sampled from 421 trees at five sites in England. Whole genomic DNA from these samples was shot-gun sequenced with short reads. Non-oak reads were extracted from these data and queried to microbial databases. Reads uniquely matching AOD-associated bacterial genomes were found to be present on trees from all five sites and included trees with active lesions, trees with historic lesions and trees without AOD symptoms. The abundance of the AOD-associated bacteria did not differ between tree health categories but did differ among sites. We conclude that the AOD-associated bacteria may be members of the normal oak microbiome, whose presence on a tree is not sufficient to cause AOD symptoms.

Disentangling the numerous processes that affect patterns of genome‐wide diversity in widespread tree species has important implications for taxonomy, conservation, and forestry. Here, we investigate the population genomic structure of Asian white birch (Betula platyphylla) in China and seek to explain it in terms of hybridization, demography and adaptation. We generate whole genome sequence data from 83 individuals across the species range in China. Combining this with an existing data set for 79 European and Russian white birches, we show a clear distinction between B. pendula and B. platyphylla, which have sometimes been lumped taxonomically. Genomic diversity of B. platyphylla in north‐western China and Central Russia is affected greatly by hybridization with B. pendula. Excluding these hybridized populations, B. platyphylla in China has a linear distribution from north‐eastern to south‐western China, along the edge of the inland mountainous region. Within this distribution, three genetic clusters are found, which we model as long diverged with subsequent episodes of gene flow. Patterns of covariation between allele frequencies and environmental variables in B. platyphylla suggest the role of natural selection in the distribution of diversity at 7609 SNPs of which 3767 were significantly differentiated among the genetic clusters. The putative adaptive SNPs are distributed throughout the genome and span 1633 genic regions. Of these genic regions, 87 were previously identified as candidates for selective sweeps in Eurasian B. pendula. We use the 7609 environmentally associated SNPs to estimate the risk of nonadaptedness for each sequenced B. platyphylla individual under a scenario of future climate change, highlighting areas where populations may be under future threat from rising temperatures.