Fig. 4: Branch-specific selection signature scans.

a Population tree is used for the population-specific selection analyses. Input consists of an “outgroup” population (America) and two “ingroup” populations (India and SE-Asia, or Europe and SE-Asia). We present the number of genes in the ingroup populations belonging to the top 1% CLR scores reported by 3P-CLR. b Venn diagram showing the genes under selection that are common between the populations of SE-Asia, India, and Europe. c Branch-specific genome-wide scan of selection: each dot represents a chromosomal locus picked by 3P-CLR for which a CLR score is calculated; loci on the top 1% CLR are shown in red. The dashed purple lines between European and Indian panels indicate common peaks of selection detected at the same genomic regions in both populations. d Genomic diversity as depicted by π (solid black lines) and Tajima’s D (solid red lines) for two selected loci: the FLK (left) and the CYP78A9 (right). FLK shows a signature of selection (low π and negative Tajima’s D) in the European population, while CYP78A9 shows a signature of selection in both Europe and India. Dashed lines indicate genome-wide averages for π (black) and Tajima’s D (red).