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 wh...

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Bibliographic Details
Published in:Genetics (Austin) 2003-11, Vol.165 (3), p.1619-1622
Main Authors: Baudry, Emmanuelle, Depaulis, Frantz
Format: Article
Language:English
Subjects:
Demographics
Genetics
homoplasmy
Mutation
Polymorphism, Genetic
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Summary: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.
ISSN:0016-6731
1943-2631
1943-2631
DOI:10.1093/genetics/165.3.1619