9.23 The PopHuman browser

While some R packages exist to compute EHH and iHS (e.g., the rehh package), they require some tricky processing of VCF files. Moreover, these statistics have already been computed genome-wide for all of the populations in the 1000 Genomes dataset, available from the PopHuman browser.

This browser lets you pull up results for several population genetic signatures. Look up the lactase (LCT) gene in the search bar, and then click Select tracks in the upper left-hand corner to choose:

iHS for the CEU (European) population
pi for the CEU population. This is a measure of nucleotide diversity, which we expect to be low in a region under historical selection

Fig. 13. iHS and \(\pi\) in the LCT region.

Note that if we compare both of these statistics to the genome-wide mean (yellow lines), we can see how dramatically they deviate from expectations in this genomic region.