Effect of Misoriented Sites on Neutrality Tests With Outgroup

Effect of Misoriented Sites on Neutrality Tests With Outgroup

Emmanuelle Baudry^a and Frantz Depaulis^a
^a Laboratoire d'Ecologie, Centre National de la Recherche Scientifique UMR 7625-EPHE, Université Pierre et Marie Curie, 75252 Paris Cedex 05, France

Corresponding author: Frantz Depaulis, Laboratoire d'Ecologie, CNRS UMR 7625-EPHE, case 237, bat A, 7 quai St. Bernard, 75252 Paris Cedex 05, France., fdepaulis{at}snv.jussieu.fr (E-mail)

Communicating editor: D. BEGUN

Several neutrality tests use outgroups to infer the ancestraland derived states for polymorphism data. However, homoplasycan result in the incorrect inference of the derived variant.We show that empirically derived rates of misorientation stronglyinfluence Fay and Wu's H-test, especially when the sample sizeis large.

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