Background and Aims In Central Europe, the drought-tolerant downy oak (Quercus pubescens) is at the northern edge of its natural distribution range, often growing in small and spatially isolated populations. Here, we elucidate how the population genetic structure of Central European Q. pubescens was shaped by geographic barriers, genetic drift and introgression with the closely related sessile oak (Q. petraea).

Methods 27 Q. pubescens populations from the northern margin of Q. pubescens’ natural distribution range were sampled. Based on 16 nuclear microsatellite markers (nSSRs), Bayesian clustering and distance-based analyses were performed to determine the intraspecific genetic structure and to identify genetic barriers. To identify drivers of introgression with Q. petraea, generalised linear models were applied to link levels of introgression with environmental conditions. To track post-glacial migration routes, the spatial distribution of haplotypes based on 8 chloroplast microsatellite markers (cpSSRs) was investigated.

Key Results Based on nSSRs, the study populations of Q. pubescens were divided into a western and an eastern genetic cluster. Within these clusters, more pronounced genetic substructure was observed in the west, probably due to a rugged topography and limited gene flow. Introgression from Q. petraea was more prevalent at wetter and north-exposed sites and in the west. The identified cpSSR haplotypes followed known migration pathways.

Conclusions Our results suggest two late-glacial refugia in or near the southwestern Alps and the southeastern Alps as potential sources for post-glacial migration. Although some genetic exchange is evident in Northern Italy, south of the Alps, the two clusters remain distinct at a large scale. Landscape features and introgression with Q. petraea shaped the genetic substructure at a smaller scale. Our study provides a comprehensive overview of the genetic structure of Q. pubescens in Central Europe, relevant for conservation.

Genotyping of nSSRs and cpSSRs: To determine the length of the amplified fragments (alleles) in base pairs (bp), capillary electrophoresis was performed using the sequencer SeqStudio Genetic Analyzer from Applied Biosystems by Thermo Fisher Scientific. The software GeneMapper® Software 6 (Applied Biosystems) was used to perform peak scoring. Exported allele lists have been stored as text files. 

Georeferenced samples: All samples have been georeferenced in the field by using a GPS device. All coordinates were stored in decimal degree (WGS 84).