Lactase haplotype diversity in the Old World

Abstract

Lactase persistence, the genetic trait in which intestinal lactase activity persists at childhood levels into adulthood, varies in frequency in different human populations, being most frequent in northern Europeans and certain African and Arabian nomadic tribes, who have a history of drinking fresh milk. Selection is likely to have played an important role in establishing these different frequencies since the development of agricultural pastoralism approximately 9,000 years ago. We have previously shown that the element responsible for the lactase persistence/nonpersistence polymorphism in humans is cis-acting to the lactase gene and that lactase persistence is associated, in Europeans, with the most common 70-kb lactase haplotype, A. We report here a study of the 11-site haplotype in 1,338 chromosomes from 11 populations that differ in lactase persistence frequency. Our data show that haplotype diversity was generated both by point mutations and recombinations. The four globally common haplotypes (A, B, C, and U) are not closely related and have different distributions; the A haplotype is at high frequencies only in northern Europeans, where lactase persistence is common; and the U haplotype is virtually absent from Indo-European populations. Much more diversity is seen in sub-Saharan Africans than in non-Africans, consistent with an "Out of Africa" model for peopling of the Old World. Analysis of recent recombinant haplotypes by allele-specific PCR, along with deduction of the root haplotype from chimpanzee sequence, allowed construction of a haplotype network that assisted in evaluation of the relative roles of drift and selection in establishing the haplotype frequencies in the different populations. We suggest that genetic drift was important in shaping the general pattern of non-African haplotype diversity, with recent directional selection in northern Europeans for the haplotype associated with lactase persistence.

Figure 1

LCT and polymorphic sites forming the lactase haplotype. Exons are shown as black bars. The series of circles underneath represent the polymorphic sites that form the haplotype.

Figure 2

Pairwise linkage disequilibrium analysis across the lactase gene. Shown are 195 pairwise D′ values for all possible combinations of six polymorphic loci in 13 populations. D′ values <0.5 are shown as a white boxes, D′ values between 0.5 and 0.8 are shown as gray boxes, and D′ values >0.8 are shown as black boxes. D′ values >0.8 differ significantly from D′ = 0 (χ² test, P<.05, no correction for multiple observations) except in those boxes labeled with a white spot, in which statistical significance is not reached because of the low the numbers of the rare allele.

Figure 3

List of all deduced LCT haplotypes. Complete list of LCT haplotypes, showing their allelic composition and frequency in the total sample set used in this study. The sites are as in figure 1 and are represented by either a blackened or an unblackened circle, which indicates whether the allele is the new or ancestral allele, respectively. Each haplotype is therefore represented as the combination of its component alleles. The ancestral allele at each site is defined by analysis of the analogous sequence of five unrelated chimpanzees. One chimpanzee was heterozygous for TG6236/7ΔΔ, so the commonest allele in the chimpanzee (6236/7TG) is taken as ancestral. The ancestral allele at A₈-552/-559A₉ cannot be deduced, because the chimpanzee sequence at this point is very different and so is arbitrarily taken as A₈. Asterisks (*) indicate definite haplotype, either by homozygosity observed in an individual, heterozygosity at only one site, or deduced from previous family studies. Number signs (#) indicate that the haplotype was present only at .01 frequency in any population. Haplotype R was only observed in one British individual of African descent but is not included in the data set. Haplotype c was deduced by the visual inspection of the genotypes of two individuals but was not identified by maximum likelihood analysis. Both haplotypes are included for the sake of completeness.

Figure 4

Simple recombinants of the four common haplotypes. The alleles at each polymorphic site are represented as in figures 1 and 2. The two additional sites tested are CATT+225ΔΔΔΔ and C+658T. The numbers of chromosomes of each haplotype analyzed by this method are shown on the right. When a circle is half blackened, both alleles were found on the haplotype defined by the 11 sites, and the two numbers shown are the numbers with each allele at the new (12th or 13th) site. The first number represents the number of chromosomes with the allele indicated by the first half of the circle, and the second number represents the number of chromosomes with the allele indicated by the second half of the circle. The probable position of the recombination is shown by a vertical bar, with the progenitor haplotypes indicated on either side. In some cases, the recombination point was localized more precisely by means of an exon 6 polymorphism (Boll et al. ; data not shown). For example both forms of haplotype E (+658C and +658T) were shown to be like haplotype C at exon 6, suggesting recombination between exon 6 and exon 17. The vertical bar is replaced by a question mark (?) where the position of recombination is ambiguous.

Figure 5

Lactase haplotype networks. A, Haplotype network showing probable phylogeny of the four common haplotypes (A, B, C, and U). Each line is annotated with its corresponding mutational change, and an arrow is shown where the directionality of the mutation is known. Mutational changes shown in bold are changes that occur only once in the network. B, Haplotype network, based on the framework of A, with circle size corresponding to the frequency of the haplotype in the population. An unblackened circle shows that none of that haplotype was observed in the population, and the smallest blackened circle represents frequencies of ⩽.1. The sub-Saharan African populations are grouped and shown here, with 79% of total haplotype diversity represented in the diagram. C, As B, with non-African populations showing 92% of total non-African haplotype diversity represented in the diagram. Non-African excludes northern European. D, As B, with northern European populations showing 98% of total northern European haplotype diversity represented in the diagram.