Effect of misoriented sites on neutrality tests with outgroup.
Several neutrality tests use outgroups to infer the ancestral and derived states for polymorphism data. However, homoplasy can result in the incorrect inference of the derived variant. We show that empirically derived rates of misorientation strongly influence Fay and Wu's H-test, especially when the sample size is large.
Baudry
Emmanuelle
E
Laboratoire d'Ecologie, Centre National de la Recherche Scientifique UMR 7625-EPHE, Université Pierre et Marie Curie, 75252 Paris 05, France.
Depaulis
Frantz
F
D009154:Mutation; D011110:Polymorphism, Genetic