Data and analyses for Thia et al. "The redlegged earth mite draft genome provides new insights into pesticide resistance evolution and demography in its invasive Australian range" submitted to Journal of Evolutionary Biology.

This repository comprises data and scripts used to replicate the analyses in this paper.

The goals of this study were to: (1) assemble a draft reference genome for Halotydeus destructor; (2) perform a comparative analysis of acetylcholinesterase genes among different agricultural arthropod pests; (3) characterise the population genetic patterns among Australian H. destructor populations; and (4) perform demographic modelling to understand the evolutionary relationships between eastern and western populations of H. destructor in Australia.

Genome assembly for Halotydeus destructor was perform using a combination of PacBio long-reads and Illumina short-reads from a single population sourced from Wantirna South, Victoria, Australia. Annotation was performed using RNAseq Illumina short-reads from populations sourced in Western Australia. The genome has been submitted to GenBank: Assembly, ASM2275052v1; Genome, GCA_022750525.1.

Comparative analyses used a variety of arthropod pest genomes sourced from GenBank. Acetylcholinesterase genes (ace) were extracted and these compared to those of H. destructor.

Population genomics of Australian H. destructor used pool-seq Illumina short-reads from populations sampled in Western Australian (western populations) and Victoria (eastern populations). Population structure among these populations, and diversity within these populations, was estimated.

Demographic analyses were performed using the forward-in-time simulator, dadi. We modelled the invasion of H. destructor into Australia and the split between eastern and western populations.

All data/script descriptions, and details for executing the analyses, are outlined in the README file, "README_Thia_2022_JEB.pdf".