Lactase persistence allele - haplotype diversity

In this paper, the authors look at the 13910C/T allele that is pretty well known to be asociated with lactase persistence (LP) in Europeans and 8 markers in the 30 kb surrounding this particular allele among a set of global populations (1611 samples in 37 populations) - looking for patterns of diversity. They identified 9 haplotypes with the LP (13910-T) allele and 14 haplotypes with the non-LP allele. They were not able to reconcile the fact that the LP allele occured on two different haplotypic backgrounds, hence they assert that the mutation arose independently. Their age estimates of the mutation on the two different haplotypes also supposedly confirm this. I still don't quite get the gist and the methods in this paper. I'd probably have to read it a few more times.
Interestingly, the French have lactase persistence rate of only 58.8% while the neighboring Basques have a rate of 91.7%! ... and southern Italians only 11%! I wonder how much the environmental component of "getting used" to lactose over one's lifespan is that accounts for the ability to use/tolerate lactose... these percentages seem very low.

Evidence of Still-Ongoing Convergence Evolution of the Lactase Persistence T-13910 Alleles in Humans

Nabil Sabri Enattah, Aimee Trudeau et al.

American Journal of Human Genetics Sept 2007

Abstract: A single-nucleotide variant, C/T-13910, located 14 kb upstream of the lactase gene (LCT), has been shown to be completely correlated with lactase persistence (LP) in northern Europeans. Here, we analyzed the background of the alleles carrying the critical variant in 1,611 DNA samples from 37 populations. Our data show that the T-13910 variant is found on two different, highly divergent haplotype backgrounds in the global populations. The first is the most common LP haplotype (LP H98) present in all populations analyzed, whereas the others (LP H8–H12), which originate from the same ancestral allelic haplotype, are found in geographically restricted populations living west of the Urals and north of the Caucasus. The global distribution pattern of LP T-13910 H98 supports the Caucasian origin of this allele. Age estimates based on different mathematical models show that the common LP T-13910 H98 allele (5,000–12,000 years old) is relatively older than the other geographically restricted LP alleles (1,400–3,000 years old). Our data about global allelic haplotypes of the lactose-tolerance variant imply that the T-13910 allele has been independently introduced more than once and that there is a still-ongoing process of convergent evolution of the LP alleles in humans.