Molecular Biology and Evolution 18:1136-1138 (2001)
© 2001 Society for Molecular Biology and Evolution
LETTER |
Haplotype Tests Using Coalescent Simulations Conditional on the Number of Segregating Sites
Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh, Scotland
Ecole Pratique des Hautes Études and Centre National de la Recherche Scientifique Unité Mixte de Recherche 7625, Université Pierre et Marie Curie, Paris, France
Recently, we proposed two neutrality tests (Depaulis and Veuille 1998
) based on haplotype number (K) and haplotype diversity (H). They relied on coalescent simulations conditional on the observed number of segregating sites (S) following the coalescent simulation procedure proposed by Hudson (1993)
. In a companion letter, Markovtsova, Marjoram, and Tavaré (2001) use an alternative approach, based on the joint distribution of K and S, and show that the corresponding tests are not independent of the population mutational parameter 
( = 4Neµ, where Ne is the effective population size and µ is the neutral mutation rate per generation). They use the classical procedure of coalescent simulations conditional on and restrict their distribution to the particular subset of genealogies consistent with a particular value of S. They show that if is extreme, the probability
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