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1 family members. Mass mating was necessary because A. gambiae breed very inefficiently as isolated pairs. The program reads phenotype and genotype information and automatically performs phenotype distribution comparisons between mosquitoes that carry a specific genotype or allele against the pooled phenotype distribution of all other family members. Under the null hypothesis of no correlation between genotype and phenotype, phenotype distributions for a genotype or allele would be random picks from the overall phenotype distribution. The nominal P value reported here is the probability that the two distributions were randomly drawn from the same parent distribution. Nominal P values were computed using the KS test, and similar values were obtained using the Wilcoxon-Mann-Whitney ranking test.
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We performed a large number of tests per family and therefore had to correct for multiple testing, The standard Bonferroni correction (number of tests performed times nominal P value) is overly conservative because the tests are not independent: The markers are linked, multiple comparisons at the same locus are correlated, and not all DNA markers are equally informative. Instead of a Bonferroni correction, we used an empirical permutation test. We created replicates of the observed sample, in which genotype and phenotype distributions were preserved, but any linkage between genotype and phenotype was removed by randomly reassigning the observed phenotypic values. We then asked how often any replicates that conformed to the null hypothesis (the independence of genotype and phenotype) produced P values in excess of the P value observed for the real data. This test preserved both the observed marker informativeness and the overall phenotype distribution.
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Linkage of the resistance allele to two distinct marker alleles, 2 and 4, could be explained by recombination between resistance and marker alleles or by multiple entry of the resistance allele into the family. An attempt to distinguish by reconstructing flanking markers, although not conclusive, appeared more consistent with the recombination hypothesis.
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We acknowledge the support of O. Doumbo and the Equipe Parasitologique (FMPOS, Mali) and the organizational assistance of S. Karambe, R. Sakai, and R. Gwadz. Supported by a grant from the National Institute of Allergy and Infectious Disease/NIH to K.D.V., a DOE/Sloan Foundation Fellowship in Computational Molecular Biology to K.M., DFG Sonderforscungbereich 544 to F.C.K., a Ph.D. Fellowship from the University of Heidelberg to J.V., and a James S. McDonnell Centennial Fellowship to L.K.
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