The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ~2.3 million single-nucleotide polymorphisms in 220 southern Africans and found that the Khoe-San diverged from other populations ≥100,000 years ago, but population structure within the Khoe-San dated back to about 35,000 years ago. Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification. We found evidence of adaptation targeting muscle function and immune response; potential adaptive introgression of protection from ultraviolet light; and selection predating modern human diversification, involving skeletal and neurological development. These new findings illustrate the importance of African genomic diversity in understanding human evolutionary history.

/pdf/genomic-variation-in-seven-khoe-san-groups-reveals-45jy12a557.pdf

Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History

https://www.cell.com/current-biology/pdf/S0960-9822(14)00319-4.pdf

Tracing Pastoralist Migrations to Southern Africa with Lactase Persistence Alleles

The extirpation of native wildlife species and widespread establishment of livestock farming has dramatically distorted large mammal herbivore communities across the globe. Ecological theory suggests that these shifts in the form and the intensity of herbivory have had substantial impacts on a range of ecosystem processes, but for most ecosystems it is impossible to quantify these changes accurately. We address these challenges using species-level biomass data from sub-Saharan Africa for both present day and reconstructed historical herbivore communities. Our analyses reveal pronounced herbivore biomass losses in wetter areas and substantial biomass increases and functional type turnover in arid regions. Fire prevalence is likely to have been altered over vast areas where grazer biomass has transitioned to above or below the threshold at which grass fuel reduction can suppress fire. Overall, shifts in the functional composition of herbivore communities promote an expansion of woody cover. Total herbivore methane emissions have more than doubled, but lateral nutrient diffusion capacity is below 5% of past levels. The release of fundamental ecological constraints on herbivore communities in arid regions appears to pose greater threats to ecosystem function than do biomass losses in mesic regions, where fire remains the major consumer.

/pdf/the-consequences-of-replacing-wildlife-with-livestock-in-mpos0fbg32.pdf

The consequences of replacing wildlife with livestock in Africa.

Lactase Persistence Alleles Reveal Partial East African Ancestry of Southern African Khoe Pastoralists

M.R. and M.S.P. co-lead the SAHGP initiative, and the project was designed and
coordinated by the core working group including M.R., M.S.P., S.B., H.S., R.R., J.R., K.S.,
P.V., N.M., F.J., S.H., and L.V. M.R. and H.S. obtained ethics approval for the study. The
data analysis team was led by S.H. (PCA; STRUCTURE and Y chromosome analysis) and
included A.C. (novel SNV characterization, LOF variant, f2, FST, SFS, and ROH analysis),
N.M. (functional analysis), F.J. (variant calling), S.A. (variant calling), G.B. (functional
annotation and data curation), E.R.C. (admixture), J.G. (functional annotation), M.J.S.D.
(functional annotation), A.M. (functional annotation, SNV characterization, data curation,
and mtDNA analysis), and D.S. (regional FST analysis, data visualization). All
authors wrote the Methods section and notes on their analyses. M.R. and A.C. drafted the
manuscript, and A.C. was responsible for coordinating Tables and Figures (including the
Supplement).

/pdf/whole-genome-sequencing-for-an-enhanced-understanding-of-4mvzdz9l10.pdf

Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans.

The origins of herding practices in southern Africa remain controversial. The first appearance of domesticated caprines in the subcontinent is thought to be c. 2000 years BP; however, the origin of this cultural development is still widely debated. Recent genetic analyses support the long-standing hypothesis of herder migration from the north, while other researchers have argued for a cultural diffusion hypothesis where the spread of herding practices took place without necessarily implicating simultaneous and large population movements. Here we document the Later Stone Age (LSA) site of Leopard Cave (Erongo, Namibia), which contains confirmed caprine remains, from which we infer that domesticates were present in the southern African region as early as the end of the first millennium BC. These remains predate the first evidence of domesticates previously recorded for the subcontinent. This discovery sheds new light on the emergence of herding practices in southern Africa, and also on the possible southward routes used by caprines along the western Atlantic coast.

/pdf/of-sheep-and-men-earliest-direct-evidence-of-caprine-4tvd3r44uf.pdf

“Of Sheep and Men”: Earliest Direct Evidence of Caprine Domestication in Southern Africa at Leopard Cave (Erongo, Namibia)

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“Of Sheep and Men”: Earliest Direct Evidence of Caprine Domestication in Southern Africa at Leopard Cave (Erongo, Namibia)