PT - JOURNAL ARTICLE
AU - Innan, Hideki
AU - Zhang, Kangyu
AU - Marjoram, Paul
AU - Tavaré, Simon
AU - Rosenberg, Noah A.
TI - Statistical Tests of the Coalescent Model Based on the Haplotype Frequency Distribution and the Number of Segregating Sites
AID - 10.1534/genetics.104.032219
DP - 2005 Mar 01
TA - Genetics
PG - 1763--1777
VI - 169
IP - 3
4099 - http://www.genetics.org/content/169/3/1763.short
4100 - http://www.genetics.org/content/169/3/1763.full
SO - Genetics2005 Mar 01; 169
AB - Several tests of neutral evolution employ the observed number of segregating sites and properties of the haplotype frequency distribution as summary statistics and use simulations to obtain rejection probabilities. Here we develop a “haplotype configuration test” of neutrality (HCT) based on the full haplotype frequency distribution. To enable exact computation of rejection probabilities for small samples, we derive a recursion under the standard coalescent model for the joint distribution of the haplotype frequencies and the number of segregating sites. For larger samples, we consider simulation-based approaches. The utility of the HCT is demonstrated in simulations of alternative models and in application to data from Drosophila melanogaster.