SDpop XY/ZW system
Dear @jos.kafer, I'm testing SDpop on a bivalve species for which the sex-determination system has been determined (ZW with homomorphic sex chromosomes) to see if it can be reliably used in other species. I run all the modes that are available and the double XY/ZW system returned to be the best (which is not so surprising, since bivalves have likely a poligenic sex determination system). However, when comparing the XY+ZW model with the single XY and ZW models, the genes that have been found to be significantly divergent between sexes are not the same (except for one). I was wondering why this happens: shouldn't I expect the XY+ZW model to return a set of genes similar to the ones of both XY and ZW models (or at least a subset)? Thank you!