Evaluation of demographic history and neutral parameterization on the performance of FST outlier tests
Lotterhos KE, Whitlock MC (2014) Molecular Ecology
Lotterhos and Whitlock find that Bayescan and FDIST, two genome scan methods that assume samples are evolutionarily independent, generate many false-postives in the case of IBD or range expansion. This effect is reduced in methods that account for non-independence, such as BAYENV2. We should stay tuned for the hierarchical version of Bayescan.
de Villemereuil P, et al. (2014) Molecular Ecology
The authors look at various types of genome scans methods including: Bayescan, BayEnv and latent factor mixed models (LFMM) in complex simulations including polygenic selection and hierarchical population structure. They find various strengths and weaknesses of the methods and suggest considering the results of the three types in concert.
Thanks to Thierry Gosselin for directing me to these articles.