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

Modeling the spatiotemporal spread of beneficial alleles using ancient genomes

Ancient genome sequencing technologies now provide the opportunity to study natural selection in unprecedented detail. Rather than making inferences from indirect footprints left by selection in present-day genomes, we can directly observe whether a given allele was present or absent in a particular region of the world at almost any period of human history within the last 10,000 years. Methods for studying selection using ancient genomes often rely on partitioning individuals into discrete time periods or regions of the world. However, a complete understanding of natural selection requires more nuanced statistical methods which can explicitly model allele frequency changes in a continuum across space and time. Here we introduce a method for inferring the spread of a beneficial allele across a landscape using two-dimensional partial differential equations. Unlike previous approaches, our framework can handle time-stamped ancient samples, as well as genotype likelihoods and pseudohaploid sequences from low-coverage genomes. We apply the method to a panel of published ancient West Eurasian genomes to produce dynamic maps showcasing the inferred spread of candidate beneficial alleles over time and space. We also provide estimates for the strength of selection and diffusion rate for each of these alleles. Finally, we highlight possible avenues of improvement for accurately tracing the spread of beneficial alleles in more complex scenarios.

Including diverse and admixed populations in genetic epidemiology research

The inclusion of ancestrally diverse participants in genetic studies can lead to new discoveries and is important to ensure equitable health care benefit from research advances. Here, members of the Ethical, Legal, Social, Implications (ELSI) committee of the International Genetic Epidemiology Society (IGES) offer perspectives on methods and analysis tools for the conduct of inclusive genetic epidemiology research, with a focus on admixed and ancestrally diverse populations in support of reproducible research practices. We emphasize the importance of distinguishing socially defined population categorizations from genetic ancestry in the design, analysis, reporting, and interpretation of genetic epidemiology research findings. Finally, we discuss the current state of genomic resources used in genetic association studies, functional interpretation, and clinical and public health translation of genomic findings with respect to diverse populations.

Evolution of Lactase Persistence: Turbo-Charging Adaptation in Growth Under the Selective Pressure of Maternal Mortality?

The emergence of the capacity to digest milk in some populations represents a landmark in human evolution, linking genetic change with a component of niche construction, namely dairying. Alleles promoting continued activity of the enzyme lactase through the life-course (lactase persistence) evolved in several global regions within the last 7,000 years. In some European regions, these alleles underwent rapid selection and must have profoundly affected fertility or mortality. Elsewhere, alleles spread more locally. However, the functional benefits underlying the rapid spread of lactase persistence remain unclear. Here, we set out the hypothesis that lactase persistence promoted skeletal growth, thereby offering a generic rapid solution to childbirth complications arising from exposure to ecological change, or to new environments through migration. Since reduced maternal growth and greater neonatal size both increase the risk of obstructed labour, any ecological exposure impacting these traits may increase maternal mortality risk. Over many generations, maternal skeletal dimensions could adapt to new ecological conditions through genetic change. However, this adaptive strategy would fail if ecological change was rapid, including through migration into new niches. We propose that the combination of consuming milk and lactase persistence could have reduced maternal mortality by promoting growth of the pelvis after weaning, while high calcium intake would reduce risk of pelvic deformities. Our conceptual framework provides locally relevant hypotheses to explain selection for lactase persistence in different global regions. For any given diet and individual genotype, the combination of lactase persistence and milk consumption would divert more energy to skeletal growth, either increasing pelvic dimensions or buffering them from worsening ecological conditions. The emergence of lactase persistence among dairying populations could have helped early European farmers adapt rapidly to northern latitudes, East African pastoralists adapt to sudden climate shifts to drier environments, and Near Eastern populations counteract secular declines in height associated with early agriculture. In each case, we assume that lactase persistence accelerated the timescale over which maternal skeletal dimensions could change, thus promoting both maternal and offspring survival. Where lactase persistence did not emerge, birth weight was constrained at lower levels, and this contributes to contemporary variability in diabetes risk.

Sahelian pastoralism from the perspective of variants associated with lactase persistence

OBJECTIVES

Archeological evidence shows that first nomadic pastoralists came to the African Sahel from northeastern Sahara, where milking is reported by ~7.5 ka. A second wave of pastoralists arrived with the expansion of Arabic tribes in 7th-14th century CE. All Sahelian pastoralists depend on milk production but genetic diversity underlying their lactase persistence (LP) is poorly understood.

MATERIALS AND METHODS

We investigated SNP variants associated with LP in 1,241 individuals from 29 mostly pastoralist populations in the Sahel. Then, we analyzed six SNPs in the neighboring fragment (419 kb) in the Fulani and Tuareg with the -13910*T mutation, reconstructed haplotypes, and calculated expansion age and growth rate of this variant.

RESULTS

Our results reveal a geographic localization of two different LP variants in the Sahel: -13910*T west of Lake Chad (Fulani and Tuareg pastoralists) and -13915*G east of there (mostly Arabic-speaking pastoralists). We show that -13910*T has a more diversified haplotype background among the Fulani than among the Tuareg and that the age estimate for expansion of this variant among the Fulani (~8.5 ka) corresponds to introduction of cattle to the area.

CONCLUSIONS

This is the first study showing that the "Eurasian" LP allele -13910*T is widespread both in northern Europe and in the Sahel; however, it is limited to pastoralists in the Sahel. Since the Fulani haplotype with -13910*T is shared with contemporary Eurasians, its origin could be in a region encompassing the Near East and northeastern Africa in a population ancestral to both Saharan pastoralists and European farmers.

Why and when was lactase persistence selected for? Insights from Central Asian herders and ancient DNA

The genetic adaptation of humans to the consumption of milk from dairying animals is one of the most emblematic cases of recent human evolution. While the phenotypic change under selection, lactase persistence (LP), is known, the evolutionary advantage conferred to persistent individuals remains obscure. One informative but underappreciated observation is that not all populations whose ancestors had access to milk genetically adapted to become lactase persistent. Indeed, Central Asian herders are mostly lactase nonpersistent, despite their significant dietary reliance on dairy products. Investigating the temporal dynamic of the -13.910:C>T Eurasian mutation associated with LP, we found that, after its emergence in Ukraine 5,960 before present (BP), the T allele spread between 4,000 BP and 3,500 BP throughout Eurasia, from Spain to Kazakhstan. The timing and geographical progression of the mutation coincides well with the migration of steppe populations across and outside of Europe. After 3,000 BP, the mutation strongly increased in frequency in Europe, but not in Asia. We propose that Central Asian herders have adapted to milk consumption culturally, by fermentation, and/or by colonic adaptation, rather than genetically. Given the possibility of a nongenetic adaptation to avoid intestinal symptoms when consuming dairy products, the puzzle then becomes this: why has LP been selected for at all?

Detecting Signatures of Positive Selection along Defined Branches of a Population Tree Using LSD

Identifying the genomic basis underlying local adaptation is paramount to evolutionary biology, and bears many applications in the fields of conservation biology, crop, and animal breeding, as well as personalized medicine. Although many approaches have been developed to detect signatures of positive selection within single populations and population pairs, the increasing wealth of high-throughput sequencing data requires improved methods capable of handling multiple, and ideally large number of, populations in a single analysis. In this study, we introduce LSD (levels of exclusively shared differences), a fast and flexible framework to perform genome-wide selection scans, along the internal and external branches of a given population tree. We use forward simulations to demonstrate that LSD can identify branches targeted by positive selection with remarkable sensitivity and specificity. We illustrate a range of potential applications by analyzing data from the 1000 Genomes Project and uncover a list of adaptive candidates accompanying the expansion of anatomically modern humans out of Africa and their spread to Europe.

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.

Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe

Since the Bronze Age, pastoralism has been a dominant subsistence mode on the Western steppe, but the origins of this tradition on the Eastern steppe are poorly understood. Here we investigate a putative early pastoralist population in northern Mongolia and find that dairy production was established on the Eastern steppe by 1300 BCE. Milk proteins preserved in dental calculus indicate an early focus on Western domesticated ruminants rather than local species, but genetic ancestry analysis indicates minimal admixture with Western steppe herders, suggesting that dairy pastoralism was introduced through adoption by local hunter-gatherers rather than population replacement.

Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH) beginning in the Eneolithic (ca. 3300–2700 BCE) profoundly transformed the genes and cultures of Europe and central Asia. Compared with Europe, however, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Late Bronze Age burials putatively associated with early pastoralism in northern Mongolia (ca. 1380–975 BCE). Genome-wide analysis reveals that they are largely descended from a population represented by Early Bronze Age hunter-gatherers in the Baikal region, with only a limited contribution (∼7%) of WSH ancestry. At the same time, however, mass spectrometry analysis of dental calculus provides direct protein evidence of bovine, sheep, and goat milk consumption in seven of nine individuals. No individuals showed molecular evidence of lactase persistence, and only one individual exhibited evidence of >10% WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. Unlike the spread of Neolithic farming in Europe and the expansion of Bronze Age pastoralism on the Western steppe, our results indicate that ruminant dairy pastoralism was adopted on the Eastern steppe by local hunter-gatherers through a process of cultural transmission and minimal genetic exchange with outside groups.

Lactase persistence may explain the paradoxical findings of high vitamin D concentrations in Europeans living in areas of low UV-B irradiation

BACKGROUND/OBJECTIVES

Vitamin D has a critical role in skeletal health and maintaining serum calcium levels. Calcium is needed for a variety of cellular and metabolic processes in the body. Large amounts of vitamin D can be produced in the skin when exposed to UV-B radiation. It is therefore a paradox that in Europe, Caucasians living in higher latitude countries, such as Scandinavia and Iceland, have higher serum vitamin D compared with those living in lower latitude. In a recent study of adult-type lactase persistence (LP), it was shown that Caucasian of European descent, who carried the C-13910T LP allele, had higher levels of total serum 25-hydroxyvitamin D compared with those who were lactase non-persistent. This was attributed to higher consumption of dairy. We postulated that the distribution of the LP C-13910T allele in Caucasian populations may explain the vitamin D concentration pattern seen in Europe.

SUBJECTS/METHODS

Baseline mean total serum 25 hydroxyvitamin D concentration from a clinical trial of post-menopausal women with osteoporosis was correlated to published LP frequencies in European populations.

RESULTS

In multiple regression analysis, mean total serum 25 hydroxyvitamin D concentrations in both winter and summer were in turn correlated to LP phenotype frequency (winter: r² = 0.51, p < 0.05; summer: r² = 0.4, p < 0.05).

CONCLUSIONS

High frequency of LP in northern Europe may explain high mean total serum 25 hydroxyvitamin D concentrations despite low UV-B radiation exposure.

Weaning practices among pastoralists: New evidence of infant feeding patterns from Bronze Age Eurasia

OBJECTIVES

This paper investigates infant feeding practices through stable carbon (δ¹³ C) and nitrogen (δ¹⁵ N) isotopic analyses of human bone collagen from Kamennyi Ambar 5, a Middle Bronze Age cemetery located in central Eurasia. The results presented are unique for the time period and region, as few cemeteries have been excavated to reveal a demographic cross-section of the population. Studies of weaning among pastoral societies are infrequent and this research adds to our knowledge of the timing, potential supplementary foods, and cessation of breastfeeding practices.

MATERIALS AND METHODS

Samples were collected from 41 subadults (<15 years) and 27 adults (15+ years). Isotopic reference sets from adult humans as well as faunal remains were utilized as these form the primary and complementary foods fed to infants.

RESULTS

Slight shifts in δ¹³ C and δ¹⁵ N values revealed that weaning was a multi-stage process (breastfeeding, weaning, and complete cessation of nursing) that began at 6 months of age, occurred over several years of early childhood, and was completed by 4 years of age.

DISCUSSION

Our results indicate that weaning was a multi-stage process that was unique among late prehistoric pastoralist groups in Eurasia that were dependent on milk products as a supplementary food. Our discussion centers on supporting this hypothesis with modern information on central and east Eurasian herding societies including the age at which complementary foods are introduced, the types of complementary foods, and the timing of the cessation of breastfeeding. Integral to this work is the nature of pastoral economies and their dependence on animal products, the impact of complementary foods on nutrition and health, and how milk processing may have affected nutrition content and digestibility of foods. This research on Eurasian pastoralists provides insights into the complexities of weaning among prehistoric pastoral societies as well as the potential for different complementary foods to be incorporated into infant diets in the past.

A study of the molecular variants associated with lactase persistence in different Ecuadorian ethnic groups

OBJECTIVE

Lactase persistence (LP) is an adaptive trait that certain human populations have acquired in response to lactose consumption in adulthood. The T-13910 variant has been reported as a causal polymorphism in Europeans. The Ecuadorian population has been described as multicultural and multiethnic, comprised of three main ethnic groups (Mestizo, Native Amerindian, and Afro-Ecuadorian). The aim of the study was to identify the molecular basis of LP in these admixed populations for the first time and determine the association between the T-13910 marker and the European ancestry proportion of each ethnic group.

METHODS

Genotyping was performed in 741 Ecuadorian individuals by sequencing a 576 bp region around the -13910 position upstream of the LCT gene. The ancestry proportions of Mestizo, Afro-Ecuadorian, and Native Amerindians were calculated using Ancestry Informative Markers and were compared with the diversity panel of the Human Genome Diversity Project.

RESULTS

LP prevalence calculated from T-13910 allele frequency in Mestizo, Afro-Ecuadorian, and Native Amerindians was 24.4%, 16%, and 12.5%, respectively. The ancestry percentage correlated to the admixture proportion of each ethnic group, and the C/T-13910 genotype frequency was influenced by the European ancestry proportion.

CONCLUSIONS

The presence of the T-13910 polymorphism in the Ecuadorian population suggested that LP was a trait introduced by European migration and inherited by admixture that occurred during the colonization of South America. This variant was not fixed in a population with a history of admixture, and its allele frequency was proportional to the ancestry proportion of each Ecuadorian ethnic group. Am. J. Hum. Biol. 28:774-781, 2016. © 2016Wiley Periodicals, Inc.

Adult lactose digestion status and effects on disease

BACKGROUND

Adult assimilation of lactose divides humans into dominant lactase-persistent and recessive nonpersistent phenotypes.

OBJECTIVES

To review three medical parameters of lactose digestion, namely: the changing concept of lactose intolerance; the possible impact on diseases of microbial adaptation in lactase-nonpersistent populations; and the possibility that the evolution of lactase has influenced some disease pattern distributions.

METHODS

A PubMed, Google Scholar and manual review of articles were used to provide a narrative review of the topic.

RESULTS

The concept of lactose intolerance is changing and merging with food intolerances. Microbial adaptation to regular lactose consumption in lactase-nonpersistent individuals is supported by limited evidence. There is evidence suggestive of a relationship among geographical distributions of latitude, sunhine exposure and lactase proportional distributions worldwide.

DISCUSSION

The definition of lactose intolerance has shifted away from association with lactose maldigestion. Lactose sensitivity is described equally in lactose digesters and maldigesters. The important medical consequence of withholding dairy foods could have a detrimental impact on several diseases; in addition, microbial adaptation in lactase-nonpersistent populations may alter risk for some diseases. There is suggestive evidence that the emergence of lactase persistence, together with human migrations before and after the emergence of lactase persistence, have impacted modern-day diseases.

CONCLUSIONS

Lactose maldigestion and lactose intolerance are not synonymous. Withholding dairy foods is a poor method to treat lactose intolerance. Further epidemiological work could shed light on the possible effects of microbial adaptation in lactose maldigesters. The evolutionary impact of lactase may be still ongoing.

Gene-environment interactions in human health: case studies and strategies for developing new paradigms and research methodologies

THE SYNERGISTIC EFFECTS OF GENES AND THE ENVIRONMENT ON HEALTH ARE EXPLORED IN THREE CASE STUDIES: adult lactase persistence, autism spectrum disorders, and the metabolic syndrome, providing examples of the interactive complexities underlying these phenotypes. Since the phenotypes are the initial targets of evolutionary processes, understanding the specific environmental contexts of the genetic, epigenetic, and environmental changes associated with these phenotypes is essential in predicting their health implications. Robust databases must be developed on the local scale to deconstruct both the population substructure and the unique components of the environment that stimulate geographically specific changes in gene expression patterns. To produce these databases and make valid predictions, new, locally focused, and information-dense models are needed that incorporate data on evolutionary ecology, environmental complexity, local geographic patterns of gene expression, and population substructure.

Latitude, sunshine, and human lactase phenotype distributions may contribute to geographic patterns of modern disease: the inflammatory bowel disease model

Countries with high lactase nonpersistence (LNP) or low lactase persistence (LP) populations have lower rates of some "western" diseases, mimicking the effects of sunshine and latitude. Inflammatory bowel disease (IBD), ie, Crohn's disease and ulcerative colitis, is putatively also influenced by sunshine. Recent availability of worldwide IBD rates and lactase distributions allows more extensive comparisons. The aim of this study was to evaluate the extent to which modern day lactase distributions interact with latitude, sunshine exposure, and IBD rates. National IBD rates, national distributions of LP/LNP, and population-weighted average national annual ultraviolet B exposure were obtained, estimated, or calculated from the literature. Negative binomial analysis was used to assess the relationship between the three parameters and IBD rates. Analyses for 55 countries were grouped in three geographic domains, ie, global, Europe, and non-Europe. In Europe, both latitude and ultraviolet B exposure correlate well with LP/LNP and IBD. In non-Europe, latitude and ultraviolet B exposure correlate weakly with LP/LNP, but the latter retains a more robust correlation with IBD. In univariate analysis, latitude, ultraviolet B exposure, and LP/LNP all had significant relationships with IBD. Multivariate analysis showed that lactase distributions provided the best model of fit for IBD. The model of IBD reveals the evolutionary effects of the human lactase divide, and suggests that latitude, ultraviolet B exposure, and LP/LNP mimic each other because LP/LNP follows latitudinal directions toward the equator. However, on a large scale, lactase patterns also follow lateral polarity. The effects of LP/LNP in disease are likely to involve complex interactions.

Positive selection of protective variants for type 2 diabetes from the Neolithic onward: a case study in Central Asia

The high prevalence of type 2 diabetes and its uneven distribution among human populations is both a major public health concern and a puzzle in evolutionary biology. Why is this deleterious disease so common, while the associated genetic variants should be removed by natural selection? The 'thrifty genotype' hypothesis proposed that the causal genetic variants were advantageous and selected for during the majority of human evolution. It remains, however, unclear whether genetic data support this scenario. In this study, we characterized patterns of selection at 10 variants associated with type 2 diabetes, contrasting one herder and one farmer population from Central Asia. We aimed at identifying which alleles (risk or protective) are under selection, dating the timing of selective events, and investigating the effect of lifestyle on selective patterns. We did not find any evidence of selection on risk variants, as predicted by the thrifty genotype hypothesis. Instead, we identified clear signatures of selection on protective variants, in both populations, dating from the beginning of the Neolithic, which suggests that this major transition was accompanied by a selective advantage for non-thrifty variants. Combining our results with worldwide data further suggests that East Asia was particularly prone to such recent selection of protective haplotypes. As much effort has been devoted so far to searching for thrifty variants, we argue that more attention should be paid to the evolution of non-thrifty variants.

Lactose intolerance: diagnosis, genetic, and clinical factors

Most people are born with the ability to digest lactose, the major carbohydrate in milk and the main source of nutrition until weaning. Approximately 75% of the world’s population loses this ability at some point, while others can digest lactose into adulthood. This review discusses the lactase-persistence alleles that have arisen in different populations around the world, diagnosis of lactose intolerance, and its symptomatology and management.

Lactase persistence may have an independent origin in Tibetan populations from Tibet, China

Milk consumption is prevalent in daily diets of Tibetans. To digest the milk sugar lactose, lactase persistence (LP) should be required. However, little is known about the genetic basis of LP in Tibetans. We screened 495 Tibetan individuals for five previously reported single-nucleotide polymorphisms (SNPs): -13907C/G (rs41525747), -13910C/T (rs4988235), -13915T/G (rs41380347), -14010G/C and -22018G/A (rs182549), which are associated with the LP in populations from a vast region surrounding Tibet. The five SNPs were nearly absent in Tibetan populations, suggesting LP likely to have an independent origin in Tibetans rather than to be introduced via gene flow from neighboring populations. We identified three novel SNPs (-13838G/A, -13906T/A and -13908C/T) in Tibetans. In particular, -13838G/A might be functional as it is located in the binding motif for HNF4α that acts as a transcription factor for intestinal gene expression. To investigate the potential association of this variant with LP, further detailed studies are required in the future.