Beja And Nilotes: Nomadic pastoralist groups in the Sudan with opposite distributions of the adult lactase phenotypes

Lactose tolerance tests with breath hydrogen determination were performed on 585 apparently healthy adolescents and adults in the Democratic Republic of the Sudan. Out of the total, 303 probands belong to the tribal group Beja, traditional nomadic pastoralists in the desert zone between the Nile and the Red Sea. The 282 Nilotes (mainly Dinka) are members of seminomadic cattle breeding tribes in the south of the Sudan. In both populations milk consumption is substantial but only in the Beja true milk dependence, sufficient to result in selective pressures in favour of the lactase persistence allele, is likely to exist. The proportion of lactose malabsorbers was 16.8% in the Beja and 74.5% in the Nilotes. The high prevalence of lactose malabsorption among the Nilotes fits into a converging gradient of lactase gene frequencies along the Nile Valley. The Beja are the first nomadic desert population in North Africa in whom a high prevalence of lactase persistence has been demonstrated on a numerically sufficient sample.     

Gene-dosage effect on intestinal lactase activity demonstrated in vivo.

The activities of the disaccharidases lactase, maltase, and sucrase were determined in upper jejunal biopsies of 65 healthy adult German males. The study was an attempt to demonstrate the gene-dosage effect on lactase activity expected from the presence of a "hypolactasia" (l) and a "lactase-persistence" (L) allele in the German population. In contrast to lactase/sucrase ratios, lactose/maltose ratios showed a trimodal distribution in proportions of presumed genotypes LL, Ll, and ll compatible with Hardy-Weinberg equilibrium. The frequency of homozygotes ll (13.8%) was similar to the average frequency of lactose malabsorbers in Germany reported in the literature. The importance of considering the lactase gene-dosage effect in population studies of lactase activity is discussed.     

Impact of Selection and Demography on the Diffusion of Lactase Persistence

Background

The lactase enzyme allows lactose digestion in fresh milk. Its activity strongly decreases after the weaning phase in most humans, but persists at a high frequency in Europe and some nomadic populations. Two hypotheses are usually proposed to explain the particular distribution of the lactase persistence phenotype. The gene-culture coevolution hypothesis supposes a nutritional advantage of lactose digestion in pastoral populations. The calcium assimilation hypothesis suggests that carriers of the lactase persistence allele(s) (LCT*P) are favoured in high-latitude regions, where sunshine is insufficient to allow accurate vitamin-D synthesis. In this work, we test the validity of these two hypotheses on a large worldwide dataset of lactase persistence frequencies by using several complementary approaches.

Methodology

We first analyse the distribution of lactase persistence in various continents in relation to geographic variation, pastoralism levels, and the genetic patterns observed for other independent polymorphisms. Then we use computer simulations and a large database of archaeological dates for the introduction of domestication to explore the evolution of these frequencies in Europe according to different demographic scenarios and selection intensities.

Conclusions

Our results show that gene-culture coevolution is a likely hypothesis in Africa as high LCT*P frequencies are preferentially found in pastoral populations. In Europe, we show that population history played an important role in the diffusion of lactase persistence over the continent. Moreover, selection pressure on lactase persistence has been very high in the North-western part of the continent, by contrast to the South-eastern part where genetic drift alone can explain the observed frequencies. This selection pressure increasing with latitude is highly compatible with the calcium assimilation hypothesis while the gene-culture coevolution hypothesis cannot be ruled out if a positively selected lactase gene was carried at the front of the expansion wave during the Neolithic transition in Europe.     

Lactase persistence in central Asia: phenotype, genotype, and evolution

The aim of the present study is to document the evolution of the lactase persistence trait in Central Asia, a geographical area that is thought to have been a region of long-term pastoralism. Several ethnic groups co-exist in this area: Indo-Iranian speakers who are traditionally agriculturist (Tajik) and Turkic speakers who used to be nomadic herders (Kazakh, Karakalpak, Kyrgyz, Turkmen). It was recently demonstrated that horse milking practice existed in the Botai culture of Kazakhstan as early as 5,500 BP ( Outram et al. 2009 ). However, the frequency of the lactase persistence trait and its genetic basis in Central Asian populations remain largely unknown. We propose here the first genotype-phenotype study of lactase persistence in Central Asia based on 183 individuals, as well as the estimation of the time of expansion of the lactase-persistence associated polymorphism. Our results show a remarkable genetic-phenotypic correlation, with the causal polymorphism being the same than in Europe (-13.910C>T, rs4988235). The lactase persistence trait is at low frequency in these populations: between 25% and 32% in the Kazakh population (traditionally herders), according to phenotype used, and between 11% and 30% in the Tajiko-Uzbek population (agriculturalists). The difference in lactase persistence between populations, even if small, is significant when using individuals concordant for both excretion of breath hydrogen and the lactose tolerance blood glucose test phenotypes (P = 0.018, 25% for Kazakh vs. 11% for Tajiko-Uzbeks), and the difference in frequency of the -13.910*T allele is almost significant (P = 0.06, 30% for Kazakhs vs. 19% for Tajiko-Uzbeks). Using the surrounding haplotype, we estimate a date of expansion of the T allele around 6,000-12,000 yrs ago, which is consistent with archaeological records for the emergence of agropastoralism and pastoralism in Central Asia.     

Distribution of physiological adult lactase phenotypes,lactose absorber and malabsorber,in Germany

Summary A total of 1805 apparently healthy, adult and adolescent Germans (1572 males and 233 females with a mean age of 20.3 years) were examined for lactose absorption capacity employing a field version of the breath hydrogen (H₂) test. The diagnostic parameter, maximal change of breath hydrogen concentration 120 or 150 min after a load of 50 g lactose, showed a bimodal distribution, separating lactose absorbers (n-1537, 85.2%) and lactose malabsorbers (n=268, 14.8%). The distribution of the adult lactase phenotypes was independent of age, sex, and educational status. The incidence of gastrointestinal symptoms after lactose administration demonstrated the incongruity of lactose malabsorption and lactose intolerance. In addition to grouping by residdence, the probands were classified according to the birthplaces of their grandparents in order to reconstruct the distribution pattern of the lactase phenotypes prior to World War I, a period of relative population stability. Considerable differences in the frequency of lactose malabsorption were found in regions corresponding to traditional ethnic groups within the German population: northwest Germany 6–9%, west and south 13–14%, southwest 23%, east (including formerly German territories east of rivers Oder and Neisse) 22%. These differences are discussed with reference to population history. The present fairly even distribution of the lactase phenotypes in West Germany is the result of internal migrations at the end of World War II.     

PCR-RFLP genotyping assay for a lactase persistence polymorphism upstream of the lactase-phlorizin hydrolase gene

The majority of the world's human population experiences a decline of lactase gene expression during maturation, so-called lactase nonpersistence. Thus, adults with lactase nonpersistence are susceptible to developing symptoms of lactose intolerance. By contrast, lactase persistence is an autosomal dominant heritable condition that results in a high level of lactase gene expression throughout adulthood and sustained lactose tolerance. Lactase persistence has recently been correlated with a single nucleotide genetic variant (a C --> T mutation) located 13,910 bases upstream from the lactase structural gene. We aimed to develop a restriction fragment length polymorphism (RFLP) method of detecting the C/T variants as a means of identifying individuals genetically inclined toward lactase persistence or nonpersistence. Genomic DNA in a 210-bp region surrounding the -13,910-bp variant site was PCR amplified with unique primers designed to avoid or mutate adjacent restriction sites. The amplified DNA was digested with a restriction enzyme, CviJI, that recognizes the base pair sequence generated by the lactase nonpersistence variant. Restriction digest gel analysis yielded DNA fragments of the expected diagnostic molecular weight sizes for individuals that were homozygote or heterozygote for the lactase persistence and nonpersistence variants. The genotypes predicted by the RFLP-based method were confirmed by DNA sequence analysis. The RFLP-based method provides a quick and noninvasive means of molecular detection of the presence or absence of the lactase persistence variant.     

A study of lactose absorption capacity in twins

Summary Lactose absorption capacity was determined by lactose tolerance tests with breath hydrogen determination in 102 healthy, adult, Hungarian pairs of twins in order to test monogenic Mendelian inheritance of the absorptive lactase phenotypes, lactose absorber and lactose malabsorber. Of the total, 52 pairs were monozygous (MZ) and 50 dizygous (DZ) twins of indentical sex. All MZ twins were concordant with respect to lactase phenotype. Among DZ twins, the distribution of lactase phenotypes was in agreement with Hardy-Weinberg expectations derived from the frequencies of the hypolactasia gene in DZ and MZ twins, and in the general Budapest population.In the second part of the study, three commonly used methods of lactose tolerance testing, the blood glucose, the blood galactose, and the breath hydrogen tests, were compared in 49 pairs of twins concordant for lactase phenotype. Blood galactose concentration showed the greatest and only significant difference between the intrapair correlation coefficients of MZ and DZ, and no overlap between lactose absorbers and lactose malabsorbers. The intrapair correlation coefficients of peak breath hydrogen concentration in MZ and DZ twins did not significantly differ from zero, but the resolution of lactase phenotypes was satisfactory. Differences in glucose absorption and concentration in lactose absorbers and malobsorbers overlapped considerably, and among lactose absorbers correlation coefficients in DZ were higher than in MZ twins. In MZ and DZ twins, the difference in concordance and constancy of lactose intolerance symptoms was not significant.     

Ancient DNA Analysis Reveals High Frequency of European Lactase Persistence Allele (T-13910) in Medieval Central Europe

Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71–80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary history of the European lactase persistence trait and its global cultural implications.     

Frequency of lactase persistence genotype in a healthy Polish population

The majority of mammals are unable to digest lactose due to post-weaning deactivation of the LCT gene, which is responsible for encoding the enzyme lactase (i.e., adult-type hypolactasia). A substitution of C with T at position −13910 bp upstream of the LCT gene has been linked to the lactase persistence phenotype in European populations. We investigated the frequency of LCT-13910C>T polymorphism in 223 blood donors from central Poland. All samples were genotyped by polymerase chain reaction and direct sequencing. The LCT-13910 T allele (lactase persistence) was present in 51% of individuals sampled from the Polish population. We did not find any non-European variants associated with lactase persistence (LCT-13907C>G, LCT-13913T>C, LCT-13915T>G), or any new polymorphisms within the sequenced region. Allele frequencies obtained are in agreement with results from other countries and confirm the unique pattern of distribution of the LCT-13910C>T genotype in Europe.     

Brief communication: Effect of nomadic subsistence practices on lactase persistence associated genetic variation in Kuwait

Lactase persistence (LP)—the ability to digest lactose in adulthood—is paradigmatic of Holocenic dietary change affecting the evolutionary trajectory of specific populations. Kuwait represents one location of high LP where the variation in associated genomic regions has not been examined. Here, we present new sequence data from a 427 bp amplicon 14 kb upstream of the LCT (lactase) gene for two Bedouin tribal populations, the Ajman and Mutran. We estimate the frequency of known LP associated alleles and discuss the impact of nomadic‐pastoralism on the associated genetic variation. We observe high frequency (56% on average) of the ?13,915*G allele in both tribes, which is consistent with the high prevalence of LP in Kuwait. Whilst LP associated alleles occur in Kuwait at a similar frequency to other regional populations, we suggest that the ?13,915*G allele frequency among the Kuwaiti Bedouin may be higher than among non‐Bedouin Kuwaitis, possibly due to greater historical reliance on milk consumption or genetic drift. Am J Phys Anthropol 152:140–144, 2013. © 2013 Wiley Periodicals, Inc.     

Prevalence of primary adult lactose malabsorption in three populations of northern China

Summary Lactose absorption capacity was examined in 641 apparently healthy adolescents and adults (447 males and 194 females with an average age of 22.9 years and an age range of 16–46 years) using a field version of the lactose tolerance test with breath hydrogen determination. In the total sample, 89 lactose absorbers and 552 lactose malabsorbers were identified. Lactose malabsorption was most frequent in a subgroup of Han (Chinese) from northeastern China (229 of 248 subjects, 92.3%). Among 198 Mongols from Inner Mongolia, there were 174 lactose malabsorbers (87.9%). The frequency of lactose malabsorption was lowest in a group of Kazakhs, traditional herders from the northwestern region of Xinjiang (149 of 195 subjects, 76.4%). Reported symptoms of lactose intolerance were significantly more frequent in lactose malabsorbers. The findings in northern Han are similar to the reported lactose malabsorption frequency in southern (mainly overseas) Chinese, and correspond with the absence of animal milk from traditional Chinese diets. The relatively low prevalence of lactose malabsorption among the Kazakhs suggests that lactose persistence may be frequent in herding pastoralist populations of southwest Asia.     

Distribution of human adult lactase phenotypes in the population of Austria

Summary A total of 528 unrelated, apparently healthy, adult and adolescent Austrians (270 females, 258 males, mean age 22.1 years) were examined for lactose absorption capacity employing a noninvasive field test based on breath hydrogen (H₂) determination. Subjects exhibiting a change of breath hydrogen concentration of less than 15 volumes per million (vpm) after a load of 50 g lactose (n=422) were classified as lactorse absorbers, 106 probands (20.1%) showing increases of breath hydrogen concentration between 16 and 111 vpm were diagnosed as lactose malabsorbers. The distribution of the lactase phenotypes was independent of age and sex. Intolerance symptoms after lactose administration were significantly more frequent in lactose malabsorbers. Grouping of probands according to the birth-places of their grandparents revealed significant differences in the distribution of the lactase phenotypes in East and West Austria (East 25%, West 15% lactose malabsorbers). These differences are discussed in the light of the population history of these regions.     

Lactase haplotype diversity in the Old World

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.     

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

The ability to digest the milk sugar lactose as an adult (lactase persistence) is a variable genetic trait in human populations. The lactase-persistence phenotype is found at low frequencies in the majority of populations in sub-Saharan Africa that have been tested, but, in some populations, particularly pastoral groups, it is significantly more frequent. Recently, a CT polymorphism located 13.9 kb upstream of exon 1 of the lactase gene (LCT) was shown in a Finnish population to be closely associated with the lactase-persistence phenotype (Enattah et al. 2002). We typed this polymorphism in 1,671 individuals from 20 distinct cultural groups in seven African countries. It was possible to match seven of the groups tested with groups from the literature for whom phenotypic information is available. In five of these groups, the published frequencies of lactase persistence are >/=25%. We found the T allele to be so rare that it cannot explain the frequency of the lactase-persistence phenotype throughout Africa. By use of a statistical procedure to take phenotyping and sampling errors into account, the T-allele frequency was shown to be significantly different from that predicted in five of the African groups. Only the Fulbe and Hausa from Cameroon possessed the T allele at a level consistent with phenotypic observations (as well as an Irish sample used for comparison). We conclude that the C-13.9kbT polymorphism is not a predictor of lactase persistence in sub-Saharan Africans. We also present Y-chromosome data that are consistent with previously reported evidence for a back-migration event into Cameroon, and we comment on the implications for the introgression of the -13.9kb*T allele.     

Retinol assessment among women and children in sahelian mobile pastoralists

Micronutrient deficiencies are widespread in developing countries, particularly in remote communities such as mobile pastoralists. The nutritional and vitamin A status of this population is not well-documented in Chad. This study assessed serum retinol levels among women and children under five-year-old in nomadic and semi-nomadic pastoralist and rural-settled communities, who are similarly exposed to risk factors such as gastrointestinal parasitic infection, anaemia and emaciation. The novel method of portable fluorometry was used for the first time to measure β-carotene and retinol levels in a pastoral nomadic area. Moderate level blood retinol deficiency (<0.7?μmol/L) was observed in 5% (CI 1-11) of nomadic, 29% (CI 13-45) of semi-nomadic and 22% (CI 8-35) of sedentary women. In children, 1% (CI 0.1-4), 17% (CI 9-25) and 28% (CI 18-39), respectively, had moderate level blood retinol deficiency. In nomadic communities, women and children had blood retinol levels close to normal. Deficiency of retinol was strongly linked with lifestyle (nomadic, semi-nomadic and settled) among women and lifestyle and age among children. The results support an ecological linkage between human retinol levels and livestock milk retinol. This study shows the feasibility of portable retinol and β-carotene measurement in human blood as well as human and animal milk under remote field conditions, but the approach requires further validation.     

Molecular diagnosis and frequencies of primary hypolactasia in populations of Russia and neighboring countries

Normally, the ability to digest milk sugar (lactose) is present in every child, but not in every adult. The decrease in lactase synthesis (hypolactasia) results in the inability to digest whole milk. Recent studies of the Finnish population have associated lactase persistence in adults with allele T of the C/T_?13910 polymorphism located upstream of the lactase gene; a 100% correlation of primary hypolactasia with genotype C/C has been proved. In this study, the allele and genotype frequencies of C/T_?13910 were determined in populations of Russia. The frequencies of genotype C/C, varying from 36.6% in Russians to 88.2% in Chukchi, were close to the published medical and epidemiological data on the hypolactasia frequencies in these populations. Genotyping was carried out by three different methods to determine the optimal one. Genotype C/C proved to be the key determinant of primary hypolactasia. It was assumed that DNA diagnosis of genotype C/C provides a predictive test to detect primary hypolactasia long before its clinical manifestation.     

Genetic signatures of strong recent positive selection at the lactase gene

In most human populations, the ability to digest lactose contained in milk usually disappears in childhood, but in European-derived populations, lactase activity frequently persists into adulthood (Scrimshaw and Murray 1988). It has been suggested (Cavalli-Sforza 1973; Hollox et al. 2001; Enattah et al. 2002; Poulter et al. 2003) that a selective advantage based on additional nutrition from dairy explains these genetically determined population differences (Simoons 1970; Kretchmer 1971; Scrimshaw and Murray 1988; Enattah et al. 2002), but formal population-genetics-based evidence of selection has not yet been provided. To assess the population-genetics evidence for selection, we typed 101 single-nucleotide polymorphisms covering 3.2 Mb around the lactase gene. In northern European-derived populations, two alleles that are tightly associated with lactase persistence (Enattah et al. 2002) uniquely mark a common (~77%) haplotype that extends largely undisrupted for >1 Mb. We provide two new lines of genetic evidence that this long, common haplotype arose rapidly due to recent selection: (1) by use of the traditional F(ST) measure and a novel test based on p(excess), we demonstrate large frequency differences among populations for the persistence-associated markers and for flanking markers throughout the haplotype, and (2) we show that the haplotype is unusually long, given its high frequency--a hallmark of recent selection. We estimate 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 we observe are among the strongest yet seen for any gene in the genome.