Haplotype based testing for a better understanding of the selective architecture

The identification of genomic regions affected by selection is one of the most important goals in population genetics. If temporal data are available, allele frequency changes at SNP positions are often used for this purpose. Here we provide a new testing approach that uses haplotype frequencies instead of allele frequencies. With this approach, less multiple testing correction is needed, which leads to tests with higher power, especially when the number of candidate haplotypes is small or moderate. Another advantage is that haplotype frequencies can often be recovered with less noise than SNP frequencies, especially under pool sequencing. For a larger number of haplotypes, we investigate methods to combine them to a moderate number of haplotype subsets. The use of haplotypes also permits a better understanding of selective signatures. For this purpose, we propose post hoc tests for the selected haplotypes and differences between their selection coefficients. Using both simulated and real data sets, we illustrate the performance and benefits of our proposed test statistics.