Ostrinia population genomics: Custom scripts and synteny mapping results

We sampled seven Ostrinia furnacalis (Guenée) populations across 23 degrees of latitude in China to elucidate the genetic basis of diapause variation and evolutionary mechanisms driving parallel clinal responses. Using pooled whole-genome sequencing (Pool-seq) data, population genomic analyses revealed hundreds of single nucleotide polymorphisms (SNP) whose allele frequencies covaried with mean diapause phenotypes along the cline. Archived on Dryad are the custom R scripts used in the population genomic analyses as well as the mapping of O. furnacalis scaffolds to Bombyx mori reference chromosomes (for visualizing population genetic statistics across chromosomes)., ,
Data:
scaff_chr_map.txt
Tab-delimited table mapping Ostrinia furnacalis scaffolds (RefSeq GCF_004193835.1) to Bombyx mori chromosomes (Silkbase ver. Jan 2017).

Scripts (Zenodo)
Written under R version 4.0.0

abba_alltopo.R

R script that calculates Patterson's D (Durand et al., 2011; Green et al., 2010) and fd (Martin et al., 2015) in windows of a given number of SNPs or basepairs to detect signatures of introgression in all possible combinations and permutations of 4 populations (tree topologies). Uses a modified sync file (see inline comments) as the input. An output file is generated for each possible tree topology.

blockjackknife.R

R script that calculates the genome-wide average Patterson's D and its confidence interval and z score by block jackknifing from an output file generated by abba_alltopo.R
blockjackknife.sh
Example usage of blockjackknife.R in bash.
dxy.R
R script that calculates genetic divergence dxy in genomic windows of a given size in basepairs for all possible p...