The following repository contains shell scripts and a genlight SNP data file presented in the article "Assessment of genetic diversity among seed transfer zones for multiple grassland plant species across Germany". (2024). Basic and Applied Ecology. doi:10.1016/j.baae.2024.11.004 1. dDocent pipeline shell scripts and configuration file Configuration_01_20cpu Configuration file for dDocent, used in 02/02a 01_dDocent_make_inputfiles_RegioDiv08_B22.sh Demultiplexing using process_radtags from Stacks (doi:10.1111/mec.12354) 01a_dDocent_make_inputfiles_command_line.sh Executable file for demultiplexing, used in 01 01b_dDocent_make_inputfiles_command_line_disable_radcheck.sh Executable file for demultiplexing, used in 01 02_dDocentRun_v294_RegioDiv_01_37G_20cpu.sh Script for starting preinstalled dDocent v. 2.9.4 02a_dDocentRun_v294_RegioDiv_03cut_37G_20cpu_2days.sh Script for starting preinstalled dDocent v. 2.9.4, first cutting 5 bases from all sequences 03_dDocent_FilterSNPs_RegioDiv_02.sh SNP filtering according to dDocent filtering tutorial and doi:10.1111/mec.14792 2. SNP genoptype file in genlight format agr.cap_work_gl.v.01.RData RData file of a genlight object called my.gl. /// GENLIGHT OBJECT ///////// // 368 genotypes, 11,341 binary SNPs, size: 7.9 Mb 633244 (15.17 %) missing data // Basic content @gen: list of 368 SNPbin @ploidy: ploidy of each individual (range: 2-2) // Optional content @ind.names: 368 individual labels @loc.names: 11341 locus labels @loc.all: 11341 alleles @chromosome: factor storing chromosomes of the SNPs @position: integer storing positions of the SNPs @pop: population of each individual (group size range: 368-368) @other: a list containing: loc.metrics loc.metrics.flags verbose history ind.metrics sample.data LocInfo.Genome clim soil TAX_work IBDIBE.UG IBDIBE.TG AMOVA.tables PCA my.gl@other$sample.data: 'data.frame': 368 obs. of 17 variables: $sample.ID : chr Unique sample identifier $sample.ID2 : num Numeric version of sample.ID $sample.label : chr Alternative unique sample identifier inclucding species, site, sample.ID.per.site $species28 : chr species identifier of the species to be sampled $species.comment : chr comment to sample $OBJECTID : int site ID $lon : num longitude $lat : num latitude $sample.name : chr full sample name including laboratory batch, index, plate position $UG : chr Seed transfer zone after Prasse et al. 2010 $TG : chr Subregion of seed transfer zone $country : chr Country, 2-digit code $ddRAD.batch : chr laboratory batch $Idx : chr index $Platte : chr plate $PlatePos : chr position on plate $cp.type : Fac affiliation of sample to cpDNA group