Genomic structure and diversity of oak populations in British Parklands

AbstractThe two predominant oak species in Britain areQuercus robur(English or pedunculate oak) andQ. petraea(sessile oak). We sequenced the whole genomes of 386 oak trees from four British parkland sites and found over 50 million nuclear single nucleotide polymorphisms (SNPs), allowing us to identify 360Q. robur, tenQ. petraeaand 16 hybrid individuals using clustering methods. ComparingQ. roburandQ. petraeatrees from Attingham Park, we found that the nuclear genomes of the two species are largely undifferentiated but identified 81 coding regions exhibiting strong interspecific differentiation. The nuclear genomes of our 360Q. roburindividuals showed no clear differentiation among the four parkland sites. Scans for selective sweeps inQ. roburhighlighted regions containing genes with putative involvement in stress tolerance, one of which was moderately differentiated fromQ. petraea. Reconstructions of past effective population sizes suggested a long population size decline in bothQ. roburandQ. petraeaover the Pleistocene, but population growth after the last glacial maximum. We assembled the whole chloroplast genomes of 287Q. robur, 8Q. petraeaand 14 hybrid trees. In a phylogenetic network, these fell into five major haplotypes, which were shared among species but differed in frequency among parkland sites. We matched our chloroplast genome haplotypes to restriction enzyme fragment haplotypes identified in older studies that had surveyed ancient woodlands in Britain and much of Europe. This suggested that the parkland populations in our study derive from local seed sources.