This paper is probably of interest to many but I don't have the insight to make a proper analysis. Just to mention that I feel deeply uncomfortable with the use of the "Sub-Saharan" term, which has so many wrong ideas attached to it, particularly the word "sub" (under, below) that it really irks me. Why not Trans-Saharan or Ultra-Saharan?, very Roman and not the least Eurocentric but definitely not just all kinds of wrong, as "Sub" is. Why not Tropical and Southern Africa?
Sub-Saharan is not just implicitly Eurocentric and almost certainly racist (sub-what?! subordinated?, sub-human maybe?) but, most importantly, it is geometrically and geographically very wrong. The South is not "under" the North: they are all on the same spheroid surface or equivalent cuasi-plane. Even a primary school student knows that!
Anyhow, this is what they have to say in minimalistic terms:
George BJ Busby et al., Admixture into and within sub-Saharan Africa. eLife 2016. Open access → LINK [doi: eLife 2016;5:e15266]
Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.
|Figure 4. (A) For each group we show the ancestry region identity of the best matching source for the first and, if applicable, second events. Events involving sources that most closely match FULAI and SEMI-BANTU are highlighted by golden and red colours, respectively. Second events can be either multiway, in which case there is a single date estimate, or two-date in which case 2ND EVENT refers to the earlier event. The point estimate of the admixture date is shown as a black point, with 95% CI shown with lines. MIXTURE MODEL: We infer the ancestry composition of each African group by fitting its copying vector as a mixture of all other population copying vectors. The coefficients of this regression sum to 1 and are coloured by ancestry region. 1ST EVENT SOURCES and 2ND EVENT SOURCES show the ancestry breakdown of the admixture sources inferred by GLOBETROTTER, coloured by ancestry region as in the key top right. (B) and (C) Comparisons of dates inferred by MALDER and GLOBETROTTER. Because the two methods sometimes inferred different numbers of events, in (B) we show the comparison based on the inferred number of events in the MALDER analysis, and in (C) for the number of events inferred by GLOBETROTTER. Point symbols refer to populations and are as in Figure 1 and source data can be found in Figure 4—source data 1|