“…Understanding the role of structural variants in adaptation and population structure has taken a more prominent role in molecular ecology (Bazzicalupo et al, 2020; Mérot, Oomen, Tigano, & Wellenreuther, 2020; Modak et al, 2021; Nelson et al, 2019; Prunier et al, 2019; Wellenreuther, Mérot, Berdan, & Bernatchez, 2019). Our analysis indicates that while haplotigs do affect structural variant detection and discovery, haplotigs, do not affect estimates of differentiation based on copy number variation.…”