The evolutionary genetics of lactase persistence in Africa and the Middle East.

Lactase, the enzyme responsible for milk digestion, is expressed in the small intestine of nearly all neonate mammals, and normally down-regulates following weaning. This is the ancestral state and in humans is described as lactase non-persistent. However, some people continue to have high expression of the enzyme for life due to a genetically inherited variation known as lactase persistence. A single nucleotide polymorphism, -13910*T was identified as the causal variation in Europeans due to a very tight association with phenotype and evidence of a functional effect in vitro. Subsequently, an apparent disparity was observed between -13910*T frequency and reported lactase persistence frequency in some African populations, raising doubts about the causal nature of the allele. Two possible explanations were proposed either -13910*T is not causal, but in Europeans is tightly linked to the true cause of lactase persistence, or, -13910*T is causal in Europeans, but the trait has evolved independently elsewhere. The primary aim of this thesis was to investigate the causes of lactase persistence in sub-Saharan Africa. The occurrence of only one -13910*T carrier out of 45 lactase persistent people from a cohort of phenotyped Sudanese individuals provided confirmation that the allele is not causal worldwide. Haplotype analysis of a 70kb region spanning the lactase gene in the phenotyped cohort and in non-European pastoralist groups provided no evidence for a shared origin with the European mutation. Resequencing of the -13910 locus led to the identification of a number of candidate SNPs -13915T>G, -13913T>C and -13907C>G, all located within 5bp of the original variant. Despite being clustered within the same OCT1 protein binding site as -13910*T, gel shift experiments revealed that the new alleles did not have a common effect on protein binding. However, -13915*G showed a significant association with lactase persistence. Resequencing of a second phenotyped cohort revealed the presence of many variant alleles at the locus, the occurrence of which is significantly higher in persistent individuals. Nearly every allele associates with an independent haplotype, providing strong evidence that multiple unrelated evolutionary events gave rise to lactase persistence. The frequency and distribution of all newly identified alleles was surveyed in more than 700 individuals from a total of 18 African and Middle Eastern populations, and gives a preliminary indication of the geographic origin of some alleles. The clustering of lactase persistence associated alleles within a single regulatory element implies that they are causal, and possible mechanisms and future approaches are discussed