Fig. 5.

Adaptive introgression from Neanderthals in a European population (CEU). We applied MaLAdapt to predict AI in overlapping 50 kb windows (step size 10 kb) along the genome of non-African populations in the 1000 Genomes Project data. Here, we show the AI prediction results of the European population (CEU), using Yoruba (YRI) as the non-introgressed outgroup and Altai Neanderthal as the introgression donor. The Y-axis shows the AI prediction score, which equals the -Log10 transformed value of [1-Pr(AI)]. Each dot in the plot represents a 50 kb window. The windows that did not reach the MaLAdapt AI threshold are colored in blue or gray depending on the chromosomes, among which the high scoring windows reflect a mix of false negatives and windows in linkage disequilibrium with AI regions. The windows detected as AI are colored in black, if they have been reported by previous studies before, or in red, if they are novel findings from this study. The labels highlight the gene names that overlap with the AI windows.