Figure 3—figure supplement 3. | Admixture into and within sub-Saharan Africa

Open accessCopyright infoDownload PDFDownload figures

Admixture into and within sub-Saharan Africa

Figure 3—figure supplement 3.

Affiliation details

Wellcome Trust Centre for Human Genetics, United Kingdom; Wellcome Trust Sanger Institute, United Kingdom; Medical Research Council Unit, The Gambia; Royal Victoria Teaching Hospital, The Gambia; Centre National de Recherche et de Formation sur le Paludisme, Burkina Faso; University of Rome La Sapienza, Italy; Navrongo Health Research Centre, Ghana; Komfo Anokye Teaching Hospital, Ghana; University of Buea, Cameroon; KEMRI-Wellcome Trust Research Programme, Kenya; Kilimanjaro Christian Medical College, Tanzania; London School of Hygiene and Tropical Medicine, United Kingdom; College of Medicine, University of Malawi, Malawi; University of Bamako, Mali
Figure 3—figure supplement 3.
Download figureOpen in new tabFigure 3—figure supplement 3. Comparison of the minimum distance to begin computing admixture LD.

For each of the 48 African populations as a target, we used ALDER to compute the minimum distance over which short-range LD is shared with each of the 47 other African and 12 Eurasian reference populations. Here we show boxplots showing the distribution of minimum inferred genetic distances (y-axis) over which LD is shared for each of the reference populations separately (x-axis). We performed two analyses using weighted LD, one using these values of the minimum distance inferred from the data, and another where this distance was forced to be 0.5cM (dotted red line). Across all African populations we observe LD correlations with other African populations at genetic distances > 0.5cM, with median values ranging between 0.7cM when GUMUZ is used as a reference to 1.4cM when FULAII is used as a reference. In fact, when we further explore the range of these values across each region separately (Figure 3—figure supplement 3), we note that, as expected, these distances are greater between more closely related groups.

DOI: http://dx.doi.org/10.7554/eLife.15266.021