I'm using Lositan with 734 SNP's for 72 individuals across a latitudinal cline, maybe structured in 2 main clusters and possibly in IBD.
If I use few iterations the envelope looks good (50K) (Fig1), but with more (>500K) looks terrible (Fig2), too ragged, and too many outliers. I've played with all parameters (#pops, force Fst, FDR,etc.) and keep getting the same,
Any ideas? Can IBD have such an strong effect?