I have noticed incorrect assignment of loci under putative balancing selection in bayescan.R
It is
dplyr::if_else(ALPHA >= 0 & Q_VALUE > 0.05, "neutral", "balancing")
which causes all loci with a negative alpha value to be considered under putative balancing selection, regardless of their q-value.
The correct way is
dplyr::if_else(ALPHA < 0 & Q_VALUE <= 0.05, "balancing", "neutral")
I do not know the original source of this mistake, but I have seen it several times in different places.
If you have doubts, see Fischer MC, Foll M, Heckel G, Excoffier L. Continental-scale footprint of balancing and positive selection in a small rodent (Microtus arvalis). PLoS One. 2014;9(11). doi:10.1371/journal.pone.0112332
I have noticed incorrect assignment of loci under putative balancing selection in bayescan.R
It is
which causes all loci with a negative alpha value to be considered under putative balancing selection, regardless of their q-value.
The correct way is
I do not know the original source of this mistake, but I have seen it several times in different places.
If you have doubts, see Fischer MC, Foll M, Heckel G, Excoffier L. Continental-scale footprint of balancing and positive selection in a small rodent (Microtus arvalis). PLoS One. 2014;9(11). doi:10.1371/journal.pone.0112332