I am interested in using Lositan for detecting loci under selection in populations of Rediviva longimanus bees. In particular I am interested in identifying regions under selection that are related to variation in leg length between the bee populations (presumably an adaptation to variation in the spur length of the host plant). I prepared two RADSeq pools where I pooled the most extreme individuals independently of population origin. Thus, I have one pool with short-legged individuals and one pool with long-legged individuals where each pool includes indivduals from ca. 4 different populations (geo distance ca. 90 km between population pairs). Also the mean neutral FST estimated is relativly high 0.5 (which might be also due to pooling different populations). My question is: can I use Lositan when I have pools and each pool includes individuals from different populations or does it not make sense at all?! I already tried Lositan with the around 19,000 SNP markers I have and got around 340 outliers which seems a bit much. When I use BayeScan I did not detect any outliers at all which made the results even more suspicious to me. I would very much appreciate any help. Thank you very much.
Best wishes, Belinda