Dataset for: Ace and ace-like genes of invasive redlegged earth mite: Copy number variation, target-site mutations, and their associations with organophosphate insensitivity

This repository contains the scripts and data required to replicate the
analyses in Thia et al.’s, “Evolution of an acetylcholinesterase gene
complex and its contribution toward organophosphate insensitivity in an
invasive mite pest”, submitted to Pest Management Science. In this work,
Thia et al. use a combination of experimental selection and pool-seq
genomic analyses to understand the genetic mechanisms underpinning
organophosphate insensitivity in the redlegged earth mite, Halotydeus
destructor. There is a special emphasis on disentangling the roles of copy
number variation and target-site mutations in the acetylcholinesterase
genes, ace, and radiated ace-like genes. There are three major analyses:
(1) an FST genome scan to identify outlier loci between alive
(insensitive) and dead (sensitive) mites; (2) an analysis of ace copy
number variation between alive and dead mites; and (3) an analysis of
candidate target-site mutations in the ace gene.