Assessment of genetic diversity among seed transfer zones for multiple grassland plant species across Germany

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