12.pbs.md

Population Branch Statistics

As a complement to the EHH-based scans for signatures of selection we also searched for signatures based on differences in allele frequency between populations. For this we used the population branch statistic (see (Yi et al. 2010)) which is designed to measure the degree to which allele frequencies at a specific locus in one population have differentiated from other populations.

Since the PBS is based on Fst we first used plink2 to calculate pairwise Fst values for all pairs of populations as follows;

plink2 --vcf Adigi.v2.filtered.vcf.gz --fst site report-variants --pheno populations.txt --allow-extra-chr --out pbs/plink2

Outputs were then converted to pbs values using an awk script

echo "IN NO SO" > pbs/plink2.pbs
paste pbs/plink2.IN.NO.fst.var pbs/plink2.IN.SO.fst.var pbs/plink2.NO.SO.fst.var | awk -f plinkfst2pbs.awk >> pbs/plink2.pbs

To plot these values as a Manhattan plot we first convert coordinates into chromosomes using RagTag

tail -n+2 pbs/plink2.pbs > pbs/plink2_noheader.pbs
python ../../../scripts/translate_coords.py pbs/plink2_noheader.pbs ../ragtag/ragtag_output/ragtag.scaffolds.agp >pbs/plink2.pbs_scaff.tsv

Figure 1: Manhattan plots showing the distribution of values of the population branch statistic (PBS) across the genome. Each plot shows PBS with a different focal population.

Yi, Xin, Yu Liang, Emilia Huerta-Sanchez, Xin Jin, Zha Xi Ping Cuo, John E Pool, Xun Xu, et al. 2010. “Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude.” Science 329 (5987): 75–78.