Host plants and host-use genes among closely related beetles

This repository includes raw material and scripts for analyses done in Bernard & Rubinoff 2026: "Host-use gene duplications and evolution covary with host diversity among closely related beetles". A csv contains host plants for each of 12 beetle species (6 bark beetles, 3 other weevils, 2 leaf beetles, and the red flour beetle), whose taxonomy has been standardized to the most current names. Multi-fastas contain genes found by homologous searches for each of 11 gene families for 9 of the beetle species (6 bark beetles, 2 other weevils, and red flour beetle). Also included are R Markdown scripts for mapping dN/dS values from HyPhy to branch lengths on gene phylogenies, comparing gene phylogenies' instability scores from MIPhy (along with csv of values from MIPhy), and calculating phylogenetic regressions.