Data from: Relict stands of Central European oaks: unravelling autochthony and genetic structure based on a multi-population study
Data files
Nov 07, 2023 version files 1.26 MB
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AQUAREL_SSR_dataset_C_Europe_Dryad.xls
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README.md
Abstract
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.
README: 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
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] 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.