Аннотация
We examine the distribution of heterozygous sites in nine European and nine
Yoruban individuals whose genomic sequences were made publicly available by
Complete Genomics. We show that it is possible to obtain detailed information
about inbreeding when a relatively small set of whole-genome sequences is
available. Rather than focus on testing for deviations from Hardy-Weinberg
genotype frequencies at each site, we analyze the entire distribution of
heterozygotes conditioned on the number of copies of the derived
(non-chimpanzee) allele. Using Levene's exact test, we reject Hardy-Weinberg in
both populations. We generalized Levene's distribution to obtain the exact
distribution of the number of heterozygous individuals given that every
individual has the same inbreeding coefficient, F. We estimated F to be 0.0026
in Europeans and 0.0005 in Yorubans, but we could also reject the hypothesis
that F was the same in each individual. We used a composite likelihood method
to estimate F in each individual and within each chromosome. Variation in F
across chromosomes within individuals was too large to be consistent with
sampling effects alone. Furthermore, estimates of F for each chromosome in
different populations were not correlated. Our results show how detailed
comparisons of population genomic data can be made to theoretical predictions.
The application of methods to the Complete Genomics data set shows that the
extent of apparent inbreeding varies across chromosomes and across individuals,
and estimates of inbreeding coefficients are subject to unexpected levels of
variation which might be partly accounted for by selection.
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