Genetic and cultural adaptations underlie the establishment of dairy pastoralism in the Tibetan Plateau

BACKGROUND

Domestication and introduction of dairy animals facilitated the permanent human occupation of the Tibetan Plateau. Yet the history of dairy pastoralism in the Tibetan Plateau remains poorly understood. Little is known how Tibetans adapted to milk and dairy products.

RESULTS

We integrated archeological evidence and genetic analysis to show the picture that the dairy ruminants, together with dogs, were introduced from West Eurasia into the Tibetan Plateau since ~ 3600 years ago. The genetic admixture between the exotic and indigenous dogs enriched the candidate lactase persistence (LP) allele 10974A > G of West Eurasian origin in Tibetan dogs. In vitro experiments demonstrate that - 13838G > A functions as a LP allele in Tibetans. Unlike multiple LP alleles presenting selective signatures in West Eurasians and South Asians, the de novo origin of Tibetan-specific LP allele - 13838G > A with low frequency (~ 6-7%) and absence of selection corresponds - 13910C > T in pastoralists across eastern Eurasia steppe.

CONCLUSIONS

Results depict a novel scenario of genetic and cultural adaptations to diet and expand current understanding of the establishment of dairy pastoralism in the Tibetan Plateau.

The influence of Scandinavian presence on Greenlandic lactase persistence

BACKGROUND

The study aims to estimate the prevalence of lactase non-persistence (LNP) among Greenlandic Inuit and Scandinavians living in Nuuk and East Greenland. The C to T transition in LCT - 13910 (rs4988235) is an autosomal inherited variant that provides the ability to lifelong lactase production, necessary to digest milk. The transition is very common in North European populations. However, LNP has only been sparsely studied in Greenland and never in Eastern Greenland, and genotype data has not previously been reported.

METHODS

Whole blood samples were collected from 535 participants, and rs4988235 was typed using a PCR-based method. Ethnicity was defined by parents' place of birth. Results were compared between East and West Greenland and Inuit and Scandinavians using Pearson's Chi² test.

RESULTS

82.2% of the participants were Inuit, and 17.8% were of Scandinavian ancestry. Among Inuit, 88.5% had LNP compared to 7.5% among Scandinavians (p < 0.001). The prevalence of LNP in Inuit varied significantly between East and West Greenland (p < 0.001). In the capital, 67.6% of Inuit had LNP compared to 98.6% in Tasiilaq and 100% in the villages around Tasiilaq.

DISCUSSION

The difference in LNP between East and West Greenland and the Inuit and Scandinavian population found in our study suggests that the original Inuit population was lactose maldigesters. Our findings suggest that the -13910 T allele was introduced into the original Inuit population by the Danes.

Nutrigenomics in the context of evolution

Nutrigenomics describes the interaction between nutrients and our genome. Since the origin of our species most of these nutrient-gene communication pathways have not changed. However, our genome experienced over the past 50,000 years a number of evolutionary pressures, which are based on the migration to new environments concerning geography and climate, the transition from hunter-gatherers to farmers including the zoonotic transfer of many pathogenic microbes and the rather recent change of societies to a preferentially sedentary lifestyle and the dominance of Western diet. Human populations responded to these challenges not only by specific anthropometric adaptations, such as skin color and body stature, but also through diversity in dietary intake and different resistance to complex diseases like the metabolic syndrome, cancer and immune disorders. The genetic basis of this adaptation process has been investigated by whole genome genotyping and sequencing including that of DNA extracted from ancient bones. In addition to genomic changes, also the programming of epigenomes in pre- and postnatal phases of life has an important contribution to the response to environmental changes. Thus, insight into the variation of our (epi)genome in the context of our individual's risk for developing complex diseases, helps to understand the evolutionary basis how and why we become ill. This review will discuss the relation of diet, modern environment and our (epi)genome including aspects of redox biology. This has numerous implications for the interpretation of the risks for disease and their prevention.

Plasticity-Led Evolution and Human Culture

Some human traits arise via organic evolution while others are acquired from the prevailing culture via a process of social learning. A mainstream interpretation is that evolution amounts to a change in the relative frequency of gene variants in a population and that culture coevolves at arm's length. Matters look different if one starts instead from the view that organisms are modified during evolution because of changes in gene expression as much as changes in the relative frequency of gene variants. Gene expression, i.e. generation of the product encoded by a gene, is not under genetic control, for it requires location- and time-specific triggers, which cannot be provided by genes. The genes present in an individual are present in every cell, hence at all locations in the individual's body and at all times during the individual's life. The necessary location- and time-specific triggers are provided internally by developmental events and conditions, or externally by environmental events and conditions, i.e. non-genetically. Socially-learned traits, having no special connection with genes, may nevertheless influence evolution, as for any trait. Like organic traits generally, socially-learned traits can be positively or negatively selected, for they similarly influence survival and reproduction. Like learned traits generally, they can play an important role in evolution by providing repeated selective pressure. The resulting evolutionary change typically affects an associated trait (e.g. adult ability to digest the sugar contained in milk), not the socially-learned trait itself (e.g. dairying), which continues under the influence of cultural processes of change.

Association of LCT -13910C>T polymorphism and hip fracture in a cohort of older adult population from Northern Spain

Hip fracture is a common health problem very frequent in the older adult population and is associated with significant morbidity, mortality, and societal costs. There are several factors that increase the risk of suffering a hip fracture, however, the effect of genetic lactase non-persistence is not clear-cut yet. For this reason, we investigated if the LCT -13910C>T polymorphism is a potential risk factor for osteoporotic hip fractures in older adult people from the Northern Spain population. A total of 740 individuals were included in this study. Of them, 364 belonged to the group of patients whit osteoporotic hip fracture while the control group consisted of 376 individuals without hip fracture. The genotypes for the LCT -13910C>T polymorphism were analyzed by using polymerase chain reaction and high resolution melting. The prevalence of the CC genotype, which is related to lactase non-persistence, did not differ significantly in both groups. Likewise, no differences were observed between groups when they were compared with regard to the C or the T allele, or when they were analyzed considering gender. Additionally, our results were compared with those obtained in a control group of 207 nonagenarian individuals originally from Northern Spain and no differences were observed. In conclusion, no significant association was observed between the LCT -13910C>T polymorphism and the risk for suffering hip fracture in the older adult population of Northern Spain.

The Eurasian lactase persistence variant LCT-13910 C/T is associated with vitamin D levels in individuals living at high latitude, more so than exposure to sunlight

Rapid selection of a genetic variant that confers continuous life-long lactase production in Europeans (LCT-13910 C/T) has been attributed to the advantages of acquiring nutrients from consuming milk without the disadvantages of lactose malabsorption. Individuals with this genetic lactase persistence (LP) variant generally consume more milk and have been shown to have higher levels of serum vitamin D. Vitamin D is the principal regulator of Ca absorption and its synthesis in skin is dependent on UVB exposure. The primary aim of the present study was to compare serum vitamin D concentrations with LP variant and to control for UVB exposure. Data from over 100 000 individuals living in Norway, a country with low UVB exposure, was retrospectively retrieved for comparison of genetic LP variant, serum 25-hydroxyvitamin D (25(OH)D) concentration and the time of year when serum samples were taken. For comparison, a similar analysis was performed with a natural dairy micronutrient, namely vitamin B₁₂. It was found that individuals with the genetic LP variant had considerably higher levels of serum 25(OH)D (P < 2 × 10^-16, Cohen's d = 0·73) but lower levels of vitamin B₁₂ (P < 2 × 10^-16, Cohen's d = 0·11), compared with genetic lactase non-persistent individuals, even when controlled for seasonality, age and sex. The difference in serum 25(OH)D levels did not diminish in summer months, showing the role of vitamin D in LP variant selection in areas of low UVB irradiation. LP variant selection advantage through acquiring another dairy micronutrient, vitamin B₁₂, was not observed.

Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait

Background

Human population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in population sizes and expansions over large distances. Here we investigate the population history of the Fulani, a pastoral population extending throughout the African Sahel/Savannah belt.

Results

Based on genome-wide analyses we propose that ancestors of the Fulani population experienced admixture between a West African group and a group carrying both European and North African ancestries. This admixture was likely coupled with newly adopted herding practices, as it resulted in signatures of genetic adaptation in contemporary Fulani genomes, including the control element of the LCT gene enabling carriers to digest lactose throughout their lives. The lactase persistence (LP) trait in the Fulani is conferred by the presence of the allele T-13910, which is also present at high frequencies in Europe. We establish that the T-13910 LP allele in Fulani individuals analysed in this study lies on a European haplotype background thus excluding parallel convergent evolution. We furthermore directly link the T-13910 haplotype with the Lactase Persistence phenotype through a Genome Wide Association study (GWAS) and identify another genomic region in the vicinity of the SPRY2 gene associated with glycaemic measurements after lactose intake.

Conclusions

Our findings suggest that Eurasian admixture and the European LP allele was introduced into the Fulani through contact with a North African population/s. We furthermore confirm the link between the lactose digestion phenotype in the Fulani to the MCM6/LCT locus by reporting the first GWAS of the lactase persistence trait. We also explored other signals of recent adaptation in the Fulani and identified additional candidates for selection to adapt to herding life-styles.

The evolutionary genetics of lactase persistence in seven ethnic groups across the Iranian plateau

Background

The ability to digest dietary lactose is associated with lactase persistence (LP) in the intestinal lumen in human. The genetic basis of LP has been investigated in many populations in the world. Iran has a long history of pastoralism and the daily consumption of dairy products; thus, we aim to assess how LP has evolved in the Iranian population. We recruited 400 adult individuals from seven Iranian ethnic groups, from whom we investigated their lactose tolerance and screened the genetic variants in their lactase gene locus.

Results

The LP frequency distribution ranged from 0 to 29.9% in the seven Iranian ethnic groups with an average value of 9.8%. The variants, − 13910*T and − 22018*A, were significantly associated with LP phenotype in Iranians. We found no evidence of hard selective sweep for − 13910*T and − 22018*A in Persians, the largest ethnic group of Iran. The extremely low frequency of − 13915*G in the Iranian population challenged the view that LP distribution in Iran resulted from the demic diffusion, especially mediated by the spread of Islam, from the Arabian Peninsula.

Conclusions

Our results indicate the distribution of LP in seven ethnic groups across the Iranian plateau. Soft selective sweep rather than hard selective sweep played a substantial role in the evolution of LP in Iranian populations.

Electronic supplementary material

The online version of this article (10.1186/s40246-019-0195-5) contains supplementary material, which is available to authorized users.

Lactase persistence genotyping on whole blood by loop-mediated isothermal amplification and melting curve analysis

BACKGROUND

The lactase persistence phenotype is controlled by a regulatory enhancer region upstream of the Lactase (LCT) gene. In northern Europe, specifically the -13910C > T variant has been associated with lactase persistence whereas other persistence variants, e.g. -13907C > G and -13915 T > G, have been identified in Africa and the Middle East. The aim of the present study was to compare a previously developed high resolution melting assay (HRM) with a novel method based on loop-mediated isothermal amplification and melting curve analysis (LAMP-MC) with both whole blood and DNA as input material.

METHODS

To evaluate the LAMP-MC method, we used 100 whole blood samples and 93 DNA samples in a two tiered study. First, we studied the ability of the LAMP-MC method to produce specific melting curves for several variants of the LCT enhancer region. Next, we performed a blinded comparison between the LAMP-MC method and our existing HRM method with clinical samples of unknown genotype.

RESULTS

The LAMP-MC method produced specific melting curves for the variants at position -13909, -13910, -13913 whereas the -13907C > G and -13915 T > G variants produced indistinguishable melting profiles.

CONCLUSION

The LAMP-MC assay is a simple method for lactase persistence genotyping and compares well with our existing HRM method.

Lactase persistence in Tunisia as a result of admixture with other Mediterranean populations

Background

The ability to digest lactose after weaning, namely, lactase persistence (LP), is encoded by polymorphisms in the MCM6 gene and varies widely in frequency among different human populations. Although, evolution of LP-related genetic variants was investigated in many groups of Sub-Saharan African, Middle Eastern, and European ancestry, only few studies have focused on populations from North Africa and no data are especially available from the Tunisian one. For this reason, there is an urgent need to investigate the frequency patterns at these loci in Tunisia since this adaptive trait is implicated in health.

Methods

Forty SNPs covering the LCT/MCM6 genes and including the two functional variants − 13,910 C > T and − 22,018 G > A were genotyped in 117 Tunisian individuals using the Sequenom Mass Array technology. The observed nucleotide and haplotype patterns of variation were then compared with those of several African, European, and Mediterranean human groups for which comparable data were publicly available. Admixture analysis on a 5 Mb genomic region surrounding the LCT/MCM6 loci was also performed by extracting genotypes from a previously generated genome-wide dataset in order to deepen the reconstruction of the evolutionary history of these loci.

Results

We found that lactase non-persistence (LNP)-related alleles and haplotypes were predominantly present in the examined population. A clear differentiation between Tunisian, African, and North European/North Italian samples was found, while the Tunisian population showed more genetic affinity to Central and South Italian groups.

Conclusions

Our study provided a first report of LP-associated alleles and haplotypes in the Tunisian population. We highlighted a gradient followed by LP diffusion from Europe to North Africa. Based on the rich historic background of Tunisia, we suggest that this adaptive trait was introduced in that geographic region by a relatively recent gene flow.

Electronic supplementary material

The online version of this article (doi:10.1186/s12263-017-0573-3) contains supplementary material, which is available to authorized users.

Lactase Non-persistence and Lactose Intolerance

PURPOSE OF REVIEW

To evaluate the clinical and nutritional significance of genetically determined lactase non-persistence and potential lactose and milk intolerance in 65-70% of the world's adult population.

RECENT FINDINGS

Milk consumption is decreasing in the USA and is the lowest in countries with a high prevalence of lactase non-persistence. The dairy industry and Minnesota investigators have made efforts to minimize the influence of lactose intolerance on milk consumption. Some lactose intolerant individuals, without co-existent irritable bowel syndrome, are able to consume a glass of milk with a meal with no or minor symptoms. The high frequency of lactase persistence in offspring of Northern European countries and in some nomadic African tribes is due to mutations in the promoter of the lactase gene in association with survival advantage of milk drinking. Educational and commercial efforts to improve calcium and Vitamin D intake have focused on urging consumption of tolerable amounts of milk with a meal, use of lowered lactose-content foods including hard cheeses, yogurt, and lactose-hydrolyzed milk products.

In Vitro Functional Analyses of Infrequent Nucleotide Variants in the Lactase Enhancer Reveal Different Molecular Routes to Increased Lactase Promoter Activity and Lactase Persistence

The genetic trait that allows intestinal lactase to persist into adulthood in some 35% of humans worldwide operates at the level of transcription, the effect being caused by cis‐acting nucleotide changes upstream of the lactase gene (LCT). A single nucleotide substitution, ‐13910 C>T, the first causal variant to be identified, accounts for lactase persistence over most of Europe. Located in a region shown to have enhancer function in vitro, it causes increased activity of the LCT promoter in Caco‐2 cells, and altered transcription factor binding. Three other variants in close proximity, ‐13907 C>G, ‐13915 T>C and ‐14010 G>C, were later shown to behave in a similar manner. Here, we study four further candidate functional variants. Two, ‐14009 T>G and ‐14011 C>T, adjacent to the well‐studied ‐14010 G>C variant, also have a clear effect on promoter activity upregulation as assessed by transfection assays, but notably are involved in different molecular interactions. The results for the two other variants (‐14028 T>C, ‐13779 G>C) were suggestive of function, ‐14028*C showing a clear change in transcription factor binding, but no obvious effect in transfections, while ‐13779*G showed greater effect in transfections but less on transcription factor binding. Each of the four variants arose on independent haplotypic backgrounds with different geographic distribution.

Association of lactase persistence genotype with milk consumption, obesity and blood pressure: a Mendelian randomization study in the 1982 Pelotas (Brazil) Birth Cohort, with a systematic review and meta-analysis

Background: Milk intake has been associated with lower blood pressure (BP) in observational studies, and randomized controlled trials suggested that milk-derived tripeptides have BP-lowering effects. Milk intake has also been associated with body mass index (BMI). Nevertheless, it is unclear whether increasing milk consumption would reduce BP in the general population.

Methods: We investigated the association of milk intake with obesity and BP using genetically-defined lactase persistence (LP) based on the rs4988235 polymorphism in a Mendelian randomization design in the 1982 Pelotas (Southern Brazil) Birth Cohort. These results were combined with published reports identified through a systematic review using meta-analysis.

Results: In the 1982 Pelotas Birth Cohort, milk intake was 42 [95% confidence interval (CI): 18; 67) ml/day higher in LP individuals. In conventional observational analysis, each 1-dl/day increase in milk intake was associated with −0.26 (95% CI: −0.33; −0.19) kg/m² in BMI and −0.31 (95% CI: −0.46; −0.16) and -0.35 (95% CI: −0.46; −0.23) mmHg in systolic and diastolic BP, respectively. These results were not corroborated when analysing LP status, but confidence intervals were large. In random effects meta-analysis, LP individuals presented higher BMI [0.17 (95% CI: 0.07; 0.27) kg/m²] and higher odds of overweight-obesity [1.09 (95% CI: 1.02; 1.17)]. There were no reliable associations for BP.

Conclusions: Our study supports that LP is positively associated with obesity, suggesting that the negative association of milk intake with obesity is likely due to limitations of conventional observational studies. Our findings also do not support that increased milk intake leads to lower BP.

Correlation of intestinal disaccharidase activities with the C/T-13910 variant and age

AIM: To correlate the C/T_-13910 variant, associated with lactase persistence/non-persistence (adult-type hypolactasia) trait, with intestinal disaccharidase activities in different age groups of the adult population.

METHODS: Intestinal biopsies were obtained from 222 adults aged 18 to 83 years undergoing upper gastrointestinal endoscopy because of unspecified abdominal complaints. The biopsies were assayed for lactase, sucrase and maltase activities and genotyped for the C/T_-13910 variant using PCR-minisequencing.

RESULTS: There was a significant correlation between lactase activity and the C/T_-13910 variant (P < 0.00001). The mean level of lactase activity among subjects with C/C_-13910 genotype was 6.86 ± 0.35 U/g, with C/T_-13910 genotype 37.8 ± 1.4 U/g, and with T/T_-13910 genotype 57.6 ± 2.4 U/g protein, showing a trimodal distribution of this enzyme activity. Significant differences were also observed in maltase activities among individuals with different C/T_-13910 genotypes (P = 0.005). In contrast, in sucrase activity, no significant differences emerged between the C/T_-13910 genotypes (P = 0.14). There were no statistical differences in lactase (P = 0.84), sucrase (P = 0.18), or maltase activity (P = 0.24) among different age groups. In the majority (> 84%) of the patients with the C/C_-13910 genotype associated with lactase non-persistence, the lactase activity was less than 10 U/g protein.

CONCLUSION: Our study demonstrates a statistically significant correlation between the C/T_-13910 genotype and lactase activity and this correlation is not affected by age in adults but the cut-off value of 20 U/g protein used for the diagnosis of lactase non-persistence might be too high.

Molecularly defined adult-type hypolactasia among working age people with reference to milk consumption and gastrointestinal symptoms

AIM: To study milk consumption and subjective milk-related symptoms in adults genotyped for adult-type hypolactasia.

METHODS: A total of 1900 Finnish adults were genotyped for the C/T_-13910 variant of adult-type hypolactasia and filled in a structured questionnaire concerning milk consumption and gastrointestinal problems.

RESULTS: The C/C_-13910 genotype of adult-type hypolactasia was present in 18% of the study population. The prevalence of the C/C_-13910 genotype was higher among subjects who were undergoing investigations because of abdominal symptoms (24%, P < 0.05). Those with the C/C_-13910 genotype drank less milk than subjects with either the C/T_-13910 or the T/T_-13910 genotype of lactase persistence (18% vs 38%; 18% vs 36%, P < 0.01). Subjects with the C/C_-13910 genotype had experienced more gastrointestinal symptoms (84%) during the preceding three-month period than those with the C/T_-13910 (79%, P < 0.05) or the T/T_-13910 genotype (78 %, P < 0.05). Only 9% (29/338) of the subjects with the C/C_-13910 genotype consumed milk and reported no symptoms from it.

CONCLUSION: Gastrointestinal symptoms are more common among adults with the C/C_-13910 genotype of adult-type hypolactasia than in those with genotypes of lactase persistence.

Lactase non-persistence and milk consumption in Estonia

AIM: To define the frequency of the C/T-13910 variant associated with lactase persistence/non-persistence trait and to analyze the milk consumption of lactase non-persistent subjects in Estonia.

METHODS: We genotyped 355 Estonians by polymerase chain reaction and direct sequencing. Milk consumption was analyzed by a questionnaire, specially developed to analyze milk consumption and abdominal complaints.

RESULTS: The frequency of the genotype of the C/C-13910 (lactase non-persistence) was found to be 24.8% in native Estonians. No other single nucleotide polymorphisms covering the region of 400 bp adjacent to the C/T-13910 variant were found. Lactase non-persistence subjects were found to consume less milk than lactase persistence subjects.

CONCLUSION: The frequency of lactase non-persistence defined by the C/C-13910 genotype confirms the results of the previous studies based on indirect methods of determining hypolactasia. Milk consumption of lactase non-persistence subjects is consistent with previously reported figures of adult-type hypolactasia in Estonia. However, lactase non-persistence does not prevent the intake of milk in many adults.