Dataset for Rapid polygenic adaptation in a wild population of ash trees under a novel fungal epidemic

Dataset for Rapid polygenic adaptation in a wild population of ash trees under a novel fungal epidemic

Code used for plotting of main figures and quantifying allelic shifts attached in the GitHub repository CareyMetheringham/MardenPark. Additional files for analysis of GEBV shifts between adults and juveniles, estimation of heritability, trends in green up and simulations of allelic shifts included as:

GEBV-regression.Rmd

heritabilityEst.R

GreeningAnalysis.R

Simulated_selection_analysis.Rmd

Distinguishing the effects of selection from genetic drift.pdf

Data files:

S1 - phenotypic measurements for adult and juvenile trees

S2 - Effect sizes for SNPs used to calculate GEBV

S3 - Allelic frequencies of sites used to calculate GEBV

related_trees.csv - Predicted parentage of trees

gebv_model_df.csv - Data used for greenup calculations in GreeningAnalysis.R

maf1.pass2.miss25.snps.only.LD.vcf - Filtered file of high MAF SNPs used for parentage estimation

unlinked_sites.csv - unlinked sites used in GEBV-regression.Rmd

ebv_table_10000_250 - table of estimated breeding values in field trial populatio, used for heritability estimation

MP_eefects_MIA_and_MAA.csv - Data for plotting Figure 3 - Estimated effect size of the major and minor allele, plus standard error on the estimate