DOI: 10.5061/dryad.4qrfj6qgs
title: Data from: Relict stands of Central European oaks: unravelling autochthony and genetic structure based on a multi-population study

description: Central European white oaks expanded rapidly after the last glacial period
 and reached their current distribution range during the early
 Holocene.  They have been an important resource of timber,
 fuelwood and animal feed for humans, who actively promoted their presence
 in forests and other landscape types at least since the early historical
 times. Besides stands with intensive management, putatively relict
 populations of three native oak species can be found on unproductive sites
 with restricted accessibility. Here, we apply chloroplast and nuclear
 microsatellite markers in order to address the autochthony of relict and
 managed stands and compare the spatial distribution of genetic variation
 between them. Based on data from more than 150 populations, we demonstrate
 that oak autochthony was preserved throughout historical times which is
 likely the result of traditional silvicultural treatment. This is
 supported by the fact that the spatial pattern of chloroplast haplotype
 distribution still reflects the post-glacial recolonization in both relict
 and old managed stands. We observed significant admixture of haplotypes
 only in stands established after the Second World War, which is
 attributable to the transfer of reproductive material used for
 afforestation. In terms of nuclear genetic variation, we observed marked
 differences among species. Quercus pubescens exhibited a pronounced
 genetic structure. Genetic drift and limited gene flow among its small and
 isolated populations in our study area might have contributed to this
 pattern. Varying extent of genetic introgression with other sympatric oak
 species could offer an additional explanation. On the contrary, the gene
 pools of Q. petraea and Q. robur are highly homogenous, displaying only
 weak isolation-by-distance. We found no significant differences of genetic
 diversity and differentiation between relict and managed stands. This
 suggests that seed transfer mostly occurred within our study area, even in
 those stands established in post-war times, verifying previous findings
 that point out limited human interference. We recommend consideration of
 population genetic structure for gene conservation, with a finer
 resolution of gene conservation units needed for Q. pubescens due to its
 spatial genetic structure. Both relict and old managed stands,
 species-pure or mixed, are suitable for conservation, as they host
 autochthonous gene pools. Coppice-with-standard management could
 contribute to preservation of autochthony. In the face of climate change,
 it is also important to maintain the evolutionary potential of the stands,
 by facilitating generative reproduction and allowing for hybridization in
 mixed stands.
description: # Data from: Relict stands of Central European oaks: unravelling
 autochthony and genetic structure based on a multi-population study
 [https://doi.org/10.5061/dryad.4qrfj6qgs](https://doi.org/10.5061/dryad.4qrfj6qgs) The dataset includes molecular genetic data (nuclear and chloroplast microsatellites) of the oak species *Quercus petraea*, *Q. robur* and *Q. pubescens* from Central Europe. These data, along with previously published data [Neophytou, Charalambos (2014). Data from: Bayesian clustering analyses for genetic assignment and study of hybridization in oaks: effects of asymmetric phylogenies and asymmetric sampling schemes [Dataset]. Dryad. [https://doi.org/10.5061/dryad.b64b4](https://doi.org/10.5061/dryad.b64b4)] were used to address the autochthony of relict and managed stands and compare the spatial distribution of genetic variation within each species. ## Description of the data and file structure The data consist of four spreadsheets: \- AQUAREL\_nSSR: includes genotypic data at 22 nuclear microsatellite \(nSSR\) loci \(two columns per locus\) described in the paper in Forest Ecology and Management\. In encompasses 2489 individuals from 64 study stands \(AQUAREL population set\) and 124 individuals from three reference populations\, one of each of *Q. petraea*, *Q. robur* and *Q. pubescens* (used to assist taxonomic identification). \- AQUAREL\_cpSSRs: includes data at 8 chloroplast microsatellite \(cpSSR\) loci \(one column per locus\) described in the paper in Forest Ecology and Management\. These 1401 individuals are a subset of those in spreadsheet AQUAREL\_nSSR from the same 64 populations\. Therefore\, geographic and species information is not repeated\. \- QREG\_M\_nSSR: includes genotypic data of 434 oaks from 12 populations of the QREG project \(QREG\_M population set\)\, genotyped at 6 nuclear SSRs\. In Neophytou & Michiels \(2013\) Forest Ecology and Management 304:89\-98\, cpSSR data were published under the same population ID\. Here\, geographic coordinates are available here at the population level only\. \- Q\_OLD\_nSSR: includes genotypic data of 96 oaks from two oak populations \(Q\_OLD population set\) at 14 nSSRs from the study published for first time in Neophytou et al\. \(2010\)\. In that study\, the two populations were designated as QpDE and QrDE\. The nSSR raw data are published here for first time\. Chloroplast SSR data from these populations were previously published in Neophytou & Michiels \(2013\) Forest Ecology and Management 304:89\-98 under the same population ID under the IDs R81 \(synonym of QpDE\) and R82 \(synonym of QrDE\)\. Geographic coordinates are available here at the population level only\. Within each spreadsheet, each individual (oak tree) is represented with one row. Common column names include: \- ID: the identification number of each tree \- Pop: the population \(forest stand\) of origin of each individual \- X and Y \(only for AQUAREL\_nSSR\, QREG\_M\_nSSR and Q\_OLD\_nSSR\): the longitude and latitude\, respectively\, in decimal degrees\. \- For AQUAREL\_nSSR\, QREG\_M\_nSSR and Q\_OLD\_nSSR: two columns per locus include the alleles as the scored DNA fragment lengths \(column names consist of locus name followed by \_1 and \_2 for the first and second allele of the locus\, respectively\)\. \- For AQUAREL\_cpSSR: one column per locus includes the allele as the scored DNA fragment length\. In spreadsheets AQUAREL\_nSSR, AQUAREL\_cpSSRs and QREG\_M\_nSSR, species identity, as revealed by a Bayesian clustering analysis based on the genotypic data, is provided under the column 'Species'. All methodological details are described in the article in Forest Ecology and Management. qpe = *Quercus petraea*, qro = *Q. robur*, qpu = *Q. pubescens*. qpe-bc, qro-bc, qpu-bc represent putative backcrosses of each species respectively, hy represent individuals which were assigned as hybrids. In the spreadsheet AQUAREL\_cpSSR, the haplotype (a unique combination of alleles across loci) is given following the nomenclature described in the published paper in Forest Ecology and Management.