March 16, 2014

Lactase persistence and pastoralism in Africa

AJHG doi:10.1016/j.ajhg.2014.02.009

Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa

Alessia Ranciaro et al.

In humans, the ability to digest lactose, the sugar in milk, declines after weaning because of decreasing levels of the enzyme lactase-phlorizin hydrolase, encoded by LCT. However, some individuals maintain high enzyme amounts and are able to digest lactose into adulthood (i.e., they have the lactase-persistence [LP] trait). It is thought that selection has played a major role in maintaining this genetically determined phenotypic trait in different human populations that practice pastoralism. To identify variants associated with the LP trait and to study its evolutionary history in Africa, we sequenced MCM6 introns 9 and 13 and ∼2 kb of the LCT promoter region in 819 individuals from 63 African populations and in 154 non-Africans from nine populations. We also genotyped four microsatellites in an ∼198 kb region in a subset of 252 individuals to reconstruct the origin and spread of LP-associated variants in Africa. Additionally, we examined the association between LP and genetic variability at candidate regulatory regions in 513 individuals from eastern Africa. Our analyses confirmed the association between the LP trait and three common variants in intron 13 (C-14010, G-13907, and G-13915). Furthermore, we identified two additional LP-associated SNPs in intron 13 and the promoter region (G-12962 and T-956, respectively). Using neutrality tests based on the allele frequency spectrum and long-range linkage disequilibrium, we detected strong signatures of recent positive selection in eastern African populations and the Fulani from central Africa. In addition, haplotype analysis supported an eastern African origin of the C-14010 LP-associated mutation in southern Africa.



Ryan said...

Any thoughts on the Fulani having the European/North Indian LP trait?

astenb said...

When looking at the dates in published research the Fulani have the oldest dates in reference to LP even compared to Europeans and Berbers. Fulani also have some type of "Berber Ancestry", It could be quite high, estimated at 30% or more at times but is not characterized in Fulani by the presence of E-M81/H1/U6.....lineages characteristic of Berber Ancestry. Instead Fulani are mostly characterized by E-m2, E-m33, and typical West African specific MTdna.

Looking at the Ancient DNA record of Europe the mutation may not be European at all.

That said Southern Africans do not carry the LP mutation East Africans share with Arabians but rather a more African specific LP mutation. The LP Mutation has yet to be found in Southern Sudanese Nilotes.