Gene sequence variation data for 3407 adult individuals from 164 range-wide populations of 7 widely distributed European forest tree species
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28 février 2023
- doi: 10.57745/DV2X0M
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Tanja Pyhäjärvi et al., « Gene sequence variation data for 3407 adult individuals from 164 range-wide populations of 7 widely distributed European forest tree species », Recherche Data Gouv, ID : 10.57745/DV2X0M
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General description This dataset contains the targeted gene sequence variation data (vcf files and their tbi index files) of seven forest tree species used in the manuscript "Synchronous effective population size changes and genetic stability of forest trees through glacial cycles". The targeted genomic regions consisted of orthologous genes from putative functions involved in local adaptation, tolerance to drought and cold, leaf phenology, etc., as well as species-specific candidate genes and randomly selected genes. For each species, between 411 and 651 genotyped trees are included, sampled across their European range in at least 19 locations. Several versions are provided. Species included: Pinus sylvestris, Picea abies, Fagus sylvatica, Populus nigra, Quercus petraea, Pinus pinaster, Betula pendula Version descriptions v.5.3: Original SNP dataset, with samples and SNPs with poor coverage or other low quality removed, organelle contigs removed (described in the SNP filtering part of the manuscript), P. nigra clones and cultivars removed, and individuals mistakenly identified as the target species removed. v.5.3.1: Master dataset derived from v.5.3, without samples with incorrect taxon assignment as indicated by genetic analysis for F. sylvatica and Q. petraea, identical to v.5.3 for the other five species. v.5.3.2: Identical to v.5.3.1 but excludes P. abies samples from populations RU_PA_19, RU_PA_20 and RU_PO. v.6.3.1: identical to v.5.3.1 but includes only four-fold degenerate sites, intron and intergenic sites, and only SNPs in low LD (1 kb windows, r < 0.5, PLINK v.1.90b4.9) v.6.3.2: identical to v.6.3.1 but excluding singletons. Note that this version is in the .ped format and each file has their accompanying .map files with locus information.