Figure 4.

Demographic reconstruction of recent admixture in the ≠Khomani San using local ancestry. (A) Local ancestry karyogram for a representative three-way admixed ≠Khomani San individual was constructed using RFMix. Haplotypes for admixed individuals were assigned to one of three possible ancestries: SAN (Namibian San), LWK (Bantu-speaking Luhya from Kenya), or CEU (Central Europeans). UNK indicates unknown ancestry (Materials and Methods). (B) Markov models implemented in TRACTs to test multiple demographic models and assess the best fit to the observed ≠Khomani haplotype distributions. Local ancestry tract lengths were inferred as in A. (C) The tract length distribution for each ancestry across all individuals was used to estimate migration time (generations ago), volume of migrants, and ancestry proportions over time. Colored dots show the observed distribution of ancestry tracts for each ancestry, solid lines show the best fit from the most likely model, and shaded areas indicate confidence intervals corresponding to ±1 SD.