Patterns of ancestry deviation across populations

To explore ancestry deviations across the full dataset, we generated a table of the top 159 signals across all populations. These 159 signals were all above a conservative significance threshold of \(-log_{10}P\geq 8\) [Fig. \ref{fig:figSharedAncestry};  Table S1], although we note again identifying the correct threshold for our approach is difficult. In just under two thirds (31) of the other 46 sub-Saharan African populations we observed no significant genome-wide deviations in ancestry. We observed multiple (\(>5\)) significant signals in just 3 populations: the Jola and Fula from the Gambia, and the Ju/hoansi from Namibia. Around a quarter (39/159; 24.5%) of the loci identified across the 48 populations, of which 32 were in the Jola, Fula and Ju/hoansi, were discounted from further analysis because of potential reciprocal copying, resulting in a final list of 114 loci, 79% of which were in the Fula, Jola, and Ju/hoansi.