Microsatellite variation and evolution of human lactase persistence

@article{Coelho2005MicrosatelliteVA,
  title={Microsatellite variation and evolution of human lactase persistence},
  author={Margarida C. Coelho and Donata Luiselli and Giorgio Bertorelle and Ana Isabel Lopes and Susana Seixas and Giovanni Destro‐Bisol and Jorge Rocha},
  journal={Human Genetics},
  year={2005},
  volume={117},
  pages={329-339}
}
The levels of haplotype diversity within the lineages defined by two single-nucleotide polymorphisms (SNPs) (−13910 C/T and −22018 G/A) associated with human lactase persistence were assessed with four fast-evolving microsatellite loci in 794 chromosomes from Portugal, Italy, Fulbe from Cameroon, São Tomé and Mozambique. Age estimates based on the intraallelic microsatellite variation indicate that the −13910*T allele, which is more tightly associated with lactase persistence, originated in… 
Convergent adaptation of human lactase persistence in Africa and Europe
TLDR
A genotype-phenotype association study in Tanzanians, Kenyans and Sudanese and identified three SNPs that are associated with lactase persistence and that have derived alleles that significantly enhance transcription from the LCT promoter in vitro, providing a marked example of convergent evolution due to strong selective pressure resulting from shared cultural traits.
Several Different Lactase Persistence Associated Alleles and High Diversity of the Lactase Gene in the Admixed Brazilian Population
TLDR
The aims of this study were to identify polymorphisms in the MCM6 region associated with the lactase persistence phenotype and to determine the distribution of LCT gene haplotypes in 981 individuals from North, Northeast and South Brazil, which shows a high variability considering the number of L CT haplotypes observed.
The Onset of Lactase Persistence in Europe
TLDR
Various studies, from archaeology to population genetics, that have shed some light on the evolution of LP in Europe are discussed, suggesting that LP arose after dairying practices had developed.
Evidence of still-ongoing convergence evolution of the lactase persistence T-13910 alleles in humans.
TLDR
The 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.
Evolutionary and molecular genetics of regulatory alleles responsible for lactase persistence
TLDR
The results show that different mechanisms lead to a disruption of the normal down-regulation of lactase in adult life, and the finding of an extended region of high linkage disequilibrium in all populations, and an extended B haplotype is discussed in relation to the methods to study selection.
World-wide distributions of lactase persistence alleles and the complex effects of recombination and selection
TLDR
New data on the frequencies of the known LP alleles in the ‘Old World’ and their haplotype lineages is reported and the results show how such suppression of recombination may have exaggerated haplotype-based measures of past selection.
Tracing the distribution and evolution of lactase persistence in Southern Europe through the study of the T‐13910 variant
TLDR
Time estimates were found to be congruent with the appearance of dairy farming in Southern Europe and the occurrence of a single introgression event, and the possible role of cultural traits and genetic history in determining these observed micro‐evolutionary patterns was discussed.
Population genomics on the origin of lactase persistence in Europe and South Asia
TLDR
It is argued that the G to A mutation at rs182549 arose earlier than 23,000 years ago, the intermediate CA haplotype ancestral to the LP-related TA haplotype is still represented by samples from Tuscans, admixed Americans and South Asians, and the great majority of G to T mutated descendants have hitchhiked since the C to T mutation was favored by local selection.
Lactose digestion and the evolutionary genetics of lactase persistence
TLDR
Access is provided to a database of worldwide distributions of lactase persistence and of the C-13910*T allele, as well as reviewing lactase molecular and population genetics and the role of selection in determining present day distributions of the lactases persistence phenotype.
...
...

References

SHOWING 1-10 OF 49 REFERENCES
The Causal Element for the Lactase Persistence/ non‐persistence Polymorphism is Located in a 1 Mb Region of Linkage Disequilibrium in Europeans
TLDR
The existence of a one megabase stretch of linkage disequilibrium in the region of LCT is reported and it is shown that the –14 kb T allele and the –22 kb A allele both occur on the background of a very extended A haplotype.
Patterns of haplotype diversity within the serpin gene cluster at 14q32.1: insights into the natural history of the α1-antitrypsin polymorphism
TLDR
Age estimates of α1-antitrypsin variants based on microsatellite variation suggest that the Z deficiency allele appeared 107–135 generations ago and could have been spread in Neolithic times, while the S mutation has an older 279- to 470-generation age, indicating that its high frequencies in Iberia did not result from a recent bottleneck and that PI*S could have originated in this region.
The use of intraallelic variability for testing neutrality and estimating population growth rate.
TLDR
It is concluded that the Delta32 allele at CCR5 and a disease-associated allele at MLH1 arose recently and have been subject to strong selection.
Identification of a variant associated with adult-type hypolactasia
TLDR
A DNA variant, C/T−13910, completely associates with biochemically verified lactase non-persistence in Finnish families and a sample set of 236 individuals from four different populations, indicating that it is very old.
Genetics of lactase persistence and lactose intolerance.
TLDR
A putative causal nucleotide change has been identified and occurs on the background of a very extended haplotype that is frequent in Northern Europeans, where lactase persistence is frequent.
Genetic signatures of strong recent positive selection at the lactase gene.
TLDR
It is estimated that strong selection occurred within the past 5,000-10,000 years, consistent with an advantage to lactase persistence in the setting of dairy farming; the signals of selection the authors observe are among the strongest yet seen for any gene in the genome.
The T allele of a single-nucleotide polymorphism 13.9 kb upstream of the lactase gene (LCT) (C-13.9kbT) does not predict or cause the lactase-persistence phenotype in Africans.
TLDR
It is concluded that the C-13.9kbT polymorphism is not a predictor of lactase persistence in sub-Saharan Africans, and Y-chromosome data is presented that is consistent with previously reported evidence for a back-migration event into Cameroon.
Genetic relationship of human populations and ethnic differences in reaction to drugs and food.
TLDR
The geographic distributions of the genes for lactose absorption and aldehyde dehydrogenase-I isozyme deficiency suggest that they have existed for a very long time in human populations and that genetic drift has been an important factor in the geographic differentiation of the frequencies of these genes.
Allelic genealogy and human evolution.
TLDR
Although the population structure prior to the late Pleistocene is less clear, the nature of Mhc polymorphism suggests that the effective size of populations leading to humans was as large as 10(5), hence, the effective population size of humans might have become somewhat smaller in most of the late pleistocene.
Estimating Effective Population Size or Mutation Rate With Microsatellites
TLDR
An estimator of θ, θ ^ F, on the basis of sample homozygosity under the single-step stepwise mutation model is developed, which is unbiased and is much more efficient than the variance-based estimator under thesingle- step stepwise mutations model.
...
...