Chromosome assignment
The current publicly available monarch genome used in this study consists of 5,397 scaffolds with an N50 value of 715.6 kB. These scaffolds were assigned to chromosomes using coverage-based chromosome assignments produced by Mongue et al.(Mongue, Nguyen, Volenikova & Walters, 2017). FST , θπ ,Td andFSTZ outliers were calculated for autosomes, Z-chromosome, and neo-Z chromosomes separately.