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

Code and attached data for plot creation and analysis of allele frequency shifts

C.L.Metheringham and R.A.Nichols

create_figure1.R

Uses the data in Supplementary Data 1 to create the stacked bar plot in Figure 1, showing the proportion of trees in each health catagory in 2019 and 2021.

gebv_mp_bglr.R and bayesb_results.R

Test if the sites identified as having large effects in the field trial (10) contributed to the visually assessed dieback damage at Marden Park, a new genomic prediction was carried out using the BGLR (V1.1)(17) package’s implementation of the BayesB algorithm (50,000 iterations with a burn in of 2000).

pca_plots.Rmd

Create Extended Data Figure 2 from PLINK output

GEBV_pheno_corr.R

Create Extended Data Figure 3

gebv_extremes_plots.Rmd

Create Extended Data Figure 4

adult_juv_gebv_shift.R

Are juvenile GEBVs significantly different from adults Accounting for ancestry of juvenile trees by unlinked sites

allele_shift_correlation.R

Correlation of effect size with alle frequency shift.

Based on methods and code by Richard A. Nichols.

Creates figure 3: To visualize the trend more clearly we grouped the loci into 200 bins (quantiles of gAf(1-f) ). The means of each bin are plotted in with an area of each point being inversely proportional to the variance in f, to convey the relative precision of the mean festimate. The line is the fitted linear regression (carried out on the individual f values).

sequoia_pedigree_subset.Rmd

Notebook used to estimate most likely parentage using sequoia.

Parentage assignment was performed with the sequoia R package (V2.3.1) (19), using a randomly selected set of 1,000 SNPs having read depth > 20, minor allele frequency > 0.4, and an estimated error rate < 0.01. Parentage assignment was run using the hermaphrodite “B” mode. DBH was used to create a proxy for the birth year of adult trees (birth year = 100 - DBH) and juvenile trees were assigned a birth year of 100. This allowed for larger, and therefore presumably older, adult trees to be assigned as parents of younger adult trees, while disallowing juveniles from being considered as parent trees. The maximum age of parents was set as 99, allowing all adult trees to be considered as parents of the juveniles. The proxy years were not intended to be an accurate estimate of tree age. Confidence of parentage assignment was estimated within sequoia by simulating genotype data based on the estimated pedigree, recalculating parentage assignment based upon simulated data and comparing the recalculated pedigree to the original pedigree. The proportion of correct assignments over multiple runs of the process gives an estimate of confidence in our parentage assignments.

parent_offspring_allele_shift.R

Uses effect_sizes.csv, gebv_site_frequencies.csv and related_trees.csv to test if allele frequencies differ from that expected from likely frequency

parent_offspring_correlation.R

Tests and plots correlation of adult GEBV and score with offspring health Create Figure 4

Data

• effect_sizes.csv

• gebv_site_frequencies.csv

• related_trees.csv

• unlinked_sites.csv

• See Suppliment 2 for details on simulated analysis and Zenodo for additional files