Eight populations [Fig. \ref{fig:figSharedAncestry}] showed evidence of significant ancestry deviation at a short haplotype in the middle of the LDB2 gene on chromosome 4. All 8 of these populations come from East Africa and are either Nilo-Saharan or Afroasiatic speakers [Table S1; Fig. \ref{fig:figLDB2}]. We sought to characterise the nature of this signal further by combining data across all 235 individuals from these 8 populations (Sudanese, Somali, Anuak, Gumuz, Ari, Tigray, Amhara and Oromo) and the two other populations from the region with nominal evidence of deviation (Afar and Wolayta). In all cases, we observed a signal of increased Khoesan ancestry [Fig. \ref{fig:figLDB2}a] and localised this to increased copying specifically from the Ju/hoansi, Xun, and Amaxhosa of southern Africa [Fig. \ref{fig:figLDB2}d]. This differs considerably from a randomly selected SNP 1.5Mb downstream, with a more usual copying profile and where the Luhya and several Eurasian groups were typically copied more. LDB2 codes for a LIM-domain binding protein, LDB2, which is a transcriptional regulator and has been linked to carotid atheroschlerosis \citep{Mm2014LimAtherosclerosis.}.