Fig. 3: Hard selective sweep in MHC-III region in Anatolian EF.

a, Haploimage of the MHC-III region and associated SweepFinder2 CLR score for the Anatolian EF, Central European EF and British Bronze Age (UK LNBA) populations. Pseudohaploid calls are shown for all samples in each population, with major alleles in yellow, minor alleles in black and missing data in white. Elevated SweepFinder2 CLR scores coincide with a region of depleted variation in the Anatolian EF population, which returns to background levels in the subsequent admixed populations. b, The estimated nucleotide diversity across the MHC-III region of the Anatolian EF (black line) and expected diversity under a hard sweep model (green line; Supplementary Text 3) relative to the underlying recombination rate in cM Mb⁻¹ (grey line on top). The two dashed red lines indicate local recombination hotspots that flank the sweep region. The close correspondence between the expected and observed genetic diversity across this region is unlikely to be a bioinformatic artefact and points to the authenticity of the signal.