9.24 Conclusion
In this lab, we used three approaches to identify selection in multi-population sequencing data.
- Using genotype data from the 1000 Genomes Project, we calculated FST, a measure of how different a variant’s allele frequency is between populations.
- We confirmed in the GGV Browser that the top FST variant shows strong population-specific AF differences.
- We confirmed in the GGV Browser that the top FST variant shows strong population-specific AF differences.
- We then calculated the population branch statistic (PBS) to identify variants under selection in a human population on Flores Island, Indonesia.
- One of the top PBS hits was in the fatty acid desaturase gene cluster (FADS).
- One of the top PBS hits was in the fatty acid desaturase gene cluster (FADS).
- Finally, we discussed extended haplotype homozygosity (EHH) and related statistics, which detect long haplotypes that result from a selective sweep.
- Using the PopHuman browser, we saw that the LCT locus – the most famous example of selection in humans – exhibits both elevated EHH and reduced genetic diversity (\(\pi\)).