#Scripts used to analyze linked selection and demography in maize

Below is a description of each script used in our linked selection manuscript. Please email Tim for further descriptions if needed.

Part 1: SFS, Genotype likelihoods, and SNP calling

fullScript_genic.sh Computes SFS, 2D-SFS, and diversity info for maize and teosinte in genic regions only.

fullScript_intergenic.sh Computes SFS, 2D-SFS, and diversity info for maize and teosinte in intergenic regions only.

fullScript_WholeGenome.sh Computes SFS, 2D-SFS, and diversity info for maize and teosinte, genome-wide.

callSNPsAngsd_maize_July.sh Calls SNPs in maize.

callSNPsAngsd_teo_july.sh Calls SNPs in teosinte.

countSingletonsMaize.R Counts maize singletons in 1000 bp windows

countSingletonsTeo.R Counts teosinte singletons in 1000 bp windows

countSingletonsMaize_downsample.R Downsamples maize to a sample size equal to teosinte and then counts maize singletons in 1000 bp windows,

Part 2: Code to study demography

ConvertSFStoDadi.R Script to convert SFS and 2D-SFS from ANGSD output format to dadi input format

realisticBottleneck.py Python function that specifies the domestication model dadi will optimize.

FINAL_DOMESTICATION_MODEL_SCRIPT_Linux.py Script to run 1,000 iterations of dadi to estimate maize and teosinte demographic model.

2d_intergenic_TIL_BKN_unpolarized.dadi Joint SFS for inputing into dadi for above script. (generated with angsd scripts and format converted with R)

MSMC A directory (with its own readme) containing scripts to run MSMC

Part 2: Code to study selection

findSubstitutions.R Identifies substitutions between maize and tripsicum, teosinte and tripsicum, teosinte and maize

exploreSubsitutions.R Explores substitutions.

TvM.vep Use Ensembl Variant Effect Predictor to estimate effects of tripsicum vs. maize substitutions.

TvT.vep Use Ensembl Variant Effect Predictor to estimate effects of tripsicum vs. teosinte substitutions.

TvMT.vep Use Ensembl Variant Effect Predictor to estimate effects of tripsicum vs. maize/teosinte (both) substitutions.

H12_array_medWindows.sh Script to calculate H12 statistic for our data. Windows are of size 200 SNPs with a step of 25 SNPs.

plotDiversity_TvM.R This script includes code to look at pairwise diversity surrounding synonymous and non-synonymous substitutions between maize and tripsicum and between teosinte and tripsicum.

plotDiversity_TvM_Singletons.R This script includes code to look at singleton diversity surrounding synonymous and non-synonymous substitutions between maize and tripsicum and between teosinte and tripsicum.

plotDiversity_Weak_Strong.R This script includes code to look at diversity surrounding synonymous and non-synonymous substitutions between maize and tripsicum at conserved and unconserved sites.

GENE_GERP.R This script includes code to look at pairwise diversity surrounding genes and conserved sites (according to GERP).

GENE_GERP_Singletons.R This script includes code to look at singleton diversity surrounding genes and conserved sites.

GENE_GERP_SINGLETONS_Downsampled.R This script investigates singleton diversity surrounding genes. It includes code to look at singletons from the downsampled set of maize.

SingletonsVsPi.R This script simulatneously investigates singleton and pairwise diversity surrounding genes.