The genome-wide distribution of ancestry deviations in the Fula

We note that because Eurasian and Khoesan haplotypes are likely to be more diverged from those of other sub-Saharan African groups we are better able to characterise them and so have more power to identify deviations concerning these ancestries. Indeed, over half (21) of the top 40 ancestry deviations observed in the Fula involve Eurasian ancestry [Supplementary Table 1; Supplementary Fig. \ref{fig:suppfulafig}], including increases of Eurasian ancestry across the HLA region on chromosome 6 (\(-log_{10}P=12.38\) ,\(\beta=1.29\)), a group of DSC genes on chromosome 18 (\(-log_{10}P=13.55\), \(\beta=1.35\)), and at APOL genes on chromosome 22 (\(-log_{10}P=13.01\), \(\beta=1.32\)). Of the non-Eurasian signals, of note are a significant increase in Central West African ancestry across the GYP genes on chromosome 4 [Fig. \ref{fig:fig2}c] (\(-log_{10}P=8.96\), \(\beta=1.13\)), encompassing a region which has recently been identified as being associated with malaria \citep{MalariaGenomicEpidemiologyNetwork2015ASelection,Leffler083634}, and which, based on a recent iHS analysis \citep{Johnson2017PatternsPopulations}, shows signs of being under natural selection. We observe an increase in Khoesan ancestry across the SERPIN genes on chromosome 18 [Fig. \ref{fig:fig2}d] (\(-log_{10}P=19.32\), \(\beta=2.98\)), one of which, SERPINB11, has previously been implicated as a target of natural selection in pastoralist groups in Africa \citep{Seixas2012LossInteractions}.
We next looked at the evidence for covariance in ancestry deviation at SNPs across the genome. As expected, in all cases we found negative covariance in ancestry at SNPs where we observed a significant deviation signal [Fig. \ref{fig:figVarCovar}a]. When one ancestry increases in frequency at a locus, it must be at the detriment to other ancestries. This association was more pronounced for more closely related ancestries. For example, the largest negative relationships were seen between East African groups [red boxes in Fig. \ref{fig:figVarCovar}a]. Interestingly, when we looked at the distribution of \(\beta\)s at significant SNPs, there was a general trend towards signals of ancestry increases , except in the case of Eurasian (yellow) and Central West African (light blue) ancestry [Fig. \ref{fig:figVarCovar}c].