How could milk-drinking have provided strong favorable selection for lactase persistence?

2.2.2 Inheritance patterns

Many genetic traits are inherited in classical Mendelian fashion. This means that both parents contribute equally because one chromosome of each pair comes from the mother and the other from the father. The transmission to the next generation of a variation on one of the numbered chromosomes (autosomes) is called autosomal inheritance. If an inherited allele always prevails over alternative ones, the inheritance pattern is called autosomal dominant. If the allele is eclipsed by the alternative, it is called autosomal recessive. Let us take the example of adults who cannot drink large amounts of milk because their lactase gene in the small intestine is turned off. This is an autosomal recessive trait for all practical purposes. This means that inheritance from only one parent is not enough to make it apparent. If someone is lactose intolerant, the trait has probably come from both parents.

Inheritance of X-linked traits is slightly different, of course. In this case all males inherit one gene dose of the trait from the mother, but none from the father (because he has contributed the Y chromosome instead). A classic example of an X-linked nutrigenetic inheritance pattern can be seen with glucose 6-phosphate (G6PD; OMIM 305900) deficiency. If males with G6PD deficiency eat broad beans or take certain medications, some of their red blood cells may break up (hemolyze). Females have the same problem only if both of their X chromosomes are affected, which happens less often. This means that the condition is usually inherited from mothers who are symptom-free carriers; rarely from fathers. Affected fathers can transmit the trait only to daughters, who will not be symptomatic unless they get a second affected X chromosome from their mother.

The inheritance of other traits follows more complex patterns. Genomic imprinting, variable numbers of nucleotide repeats, copy number variants, multilocus traits, and mosaicism are mechanisms that explain deviations from the orthodox Mendelian pattern of inheritance.

Let’s look at an example of two independently inherited traits in adults: the ability to drink significant amounts of milk (a cup or more at a time) and the ability to drink a can of sugar-containing soda without adverse effects (Figure 2.7). Milk contains lactose, large quantities of which (for instance the 12 g in one 240 mL glass) cause unpleasant digestive problems unless lactase is active in the small intestine of the drinker. Half of the sugar in soda consists of fructose (for instance 17 g in one 368 mL can), which triggers life-threatening hypoglycemia in people without a functional copy of the fructoaldolase gene (ALDOB; OMIM 612724) encoding fructose-1,6-bisphosphate aldolase (EC 4.1.2.13). Adverse effects of either lactose or fructose consumption are recessive traits, which means that they occur only when both of the gene copies inherited from the mother and father provide inadequate amounts of functional enzyme. The law of independent assortment holds true in this example. The figure below shows the outcome (phenotype) when children inherit a particular set of alleles from each parent. If, for instance, the father provides the allele for milk intolerance (I), and the mother contributes the allele for milk tolerance (L), the child will have both an “l” and an “L” allele. Because the “l” allele is recessive, the “L” allele wins out and the child will be able to drink milk. Review some parental combinations and ask yourself (without looking) what the outcome (phenotype) will be in the child.

Along those lines, consider the following example. The father is homozygous for the lactose intolerance allele (due to lack of lactase persistence) and has a problem with drinking milk (Figure 2.8). The mother is homozygous for the fructose-intolerance allele (due to defective aldolase B) and gets low blood sugar (hypoglycemia) after drinking sugar-sweetened soda. Now, because both alleles are recessive, any children resulting from this union will be able to drink both milk and sugar-sweetened soda.

Mendelian principles of heredity

Law of independent assortment

Traits are inherited independently of each other.

In the year 1866, Gregor Mendel presented in lectures and published proceedings his insightful formulation of the two basic principles of inheritance, which established the scientific study of genetics. It took several decades until the significance of his concepts was recognized, but they then guided the rapid growth of genetic research.

On the other hand, if both parents were heterozygous for both traits, there would be a 25% chance that a child would not be able to drink milk and a 25% chance that she could not tolerate the soda. Multiplication of the individual likelihoods (0.25 × 0.25 = 0.0625) indicates that one child in 16 from such a heterozygous couple will not be able to tolerate either milk or soda.

It is important to understand that traits are inherited independently only if they derive from genes on different chromosomes or at different ends of the same chromosome. Genes located near each other are often inherited together as explained in more detail below.

Analysis of a trait in multigenerational families is the most direct way to determine the mode of inheritance. An individual’s presentation (phenotype) will then depend on how critical the single-strand DNA variant is for the trait. If a trait becomes apparent even when the responsible variant is present only on one of the two DNA strands in a chromosome, it is called a dominant trait. If it takes two copies to show, it is called a recessive trait. Rare metabolic diseases (inborn errors of metabolism) such as phenylketonuria (PKU) or abetalipoproteinemia are usually recessive. This means that a single functional DNA copy can do the job and the trait becomes apparent only when both copies are altered.

Children

A review of reported data on diverse populations support the conclusion that in later childhood and adolescence an important transition in lactose digestion occurs. Below 3 years of age there is lactase persistence. Between 3 and 11 years of age the beginning of a genetically controlled lactose nonpersistence is recognized. Older children and young adults are increasingly unable to digest even modest amounts of lactose. This results in increased symptom production, recognition of discomfort, and avoidance of lactose-containing products that provoke symptoms (Table 1).

Table 1. Genetically determined lactase levels in healthy individuals by age and lactase persistence

A progressive decrease in lactase is noted from approximately 1–5 years of age through adolescence. Reported rates in United States African-American children ranged from 27% lactose maldigestion following lactose testing using a lactose load equivalent to two 8-ounce glasses of milk at 1–2 years to 74% in 11–12-year-old children. The progressive decrease in the ability to hydrolyze a lactose challenge was observed in children of both high and low socioeconomic status. Studies in white children 1–12 years of age identified only 17% of children maldigesting a lactose challenge. Signs and symptom production associated with a reduction in lactose digestion in a child population is difficult to measure due to the nature of the symptoms being reported and the signs observed and the subjective nature of the reports. This is reinforced by a report of 21 African-American girls of 11–15 years of age indicating 82% had evidence of lactose maldigestion with reports of gastrointestinal symptoms being negligible and breath hydrogen excretion, while remaining high, varied between two time periods. Consistent with the above data, milk consumption studies, both observed and reported, suggest a progressive decline in milk intake with increasing age in the African-American population of children and parallel reports in children from other populations with a high prevalence of lactose maldigestion (Table 2).

Table 2. Patterns of lactose digestion by lactase status

Sidney, Phillips, Paige & Bayless.

Phenotypic lactase nonpersistence needs to be distinguished from secondary lactose maldigestion and intolerance as a result of a variety of other conditions. Secondary lactose maldigestion can be observed with diarrheal disease and infection, celiac disease, allergic enteropathy, Crohns’ disease, chemotherapy, radiation, and small bowel resection.

Genomic Testing

Genomic testing requires a single blood sample and avoids the diet restrictions, lengthy collection regimen, and potential for abdominal symptoms that are associated with using an oral lactose challenge. The LCT gene on chromosome 2 encodes for the enzyme LPH, and the wild type is associated with lactase nonpersistence. Lactase persistence is associated with two polymorphisms on the enhancer region upstream from LCT, C/T13910 and G/A22018. Heterozygotes are considered to have lactase persistence but with intermediate lactase activity. Homozygotes T/T13910 and G/G22018 have the lactase persistence genotype, whereas C/C and G/G homozygotes carry the wild-type nonpersistence genotype. Genomic testing, although useful, only establishes a lactase enzyme deficiency, the presence of which does not always lead to lactose intolerance symptoms. Heterozygotes, although considered carriers of lactase persistence genotyping, can have bouts of impaired lactase activity due to stress or infection, rendering intermittent bouts of lactose intolerance.83 Therefore testing for lactose malabsorption through an objective measure of lactose malabsorption, such as hydrogen breath testing, is still warranted.84

Genetics

Lactase is expressed robustly by mammalian small intestinal absorptive cells and in very low levels in the colon during fetal development. Humans are born with high levels of lactase activity. However, in most populations, this lactase activity declines after weaning, resulting in diminished lactase expression in the small intestine. Some individuals, specifically descendants from populations that have traditionally practiced dairy farming, maintain the ability to digest milk and other dairy products into adulthood. Genetic studies suggest that within the last 10 000 years the mutations associated with lactase persistence have reached significant levels in human populations. Therefore, lactase persistence is sometimes viewed as an example of recent human evolution (Simoons, 1969).

Studies to determine the prevalence of lactase persistence have been conducted. Thus, global distribution of lactase persistence is well understood. The decline in lactase expression occurs in most ethnic groups with the exception of Caucasian populations from Northern Europe, some Middle Eastern populations, and the Masai tribe of Central Africa (Sahi, 1994). There are a high proportion of lactose digesters in northwestern Europe, Northern India, and in other dairy farming populations in the Middle East and Central Africa (Sahi, 1994). A very low incidence of lactase digesters was found among Eastern and Southern Asians, most Africans, and native populations of the Americas and the Pacific. Modest numbers of lactose digesters are found in Southern and Eastern Europe. Lactase persistence is closely linked to places of ancestral origin in North and South America, Australia, and New Zealand. For example, white Australians resemble their European counterparts in lactase persistence, whereas Native Australians are almost entirely lactose intolerant (Simoons, 1969). Differences in the ratio of a mix in Spanish and Indian ancestry in some individuals may also explain regional differences in Mexico (Rosado et al., 1994). In the United States, maldigestion is typically seen in groups of Chinese, Native American, and African ancestry (McCracken, 1971) (Figure 2).

Mutation and Natural Selection: The Case of Lactase Persistence

Lactase is the enzyme responsible for the digestion of the milk sugar called lactose. Lactase production decreases after the weaning phase in most humans, at which point the typical individual becomes lactose intolerant and experiences digestive upset (gas, bloating, and/or diarrhea) upon the consumption of fresh milk. Some people, however, continue to produce lactase into adulthood, a trait known as lactase persistence, or LP. LP is a genetically controlled trait that is found at moderate to high frequencies in European (particularly northern), some African, Middle Eastern, and Southern Asian populations.4

It turns out that the condition has evolved independently in at least four places around the globe and a number of different mutations have been found in association with the LP trait. What explains the high frequency of LP alleles in only certain populations? Genetic drift and gene flow have probably played a role, but here is a case in which natural selection is a more compelling candidate. Age estimates in terms of the antiquity of lactase persistence-associated alleles coincide with those for the origins of animal domestication and the cultural practice of dairying.5 Though humans were likely consuming milk products before these LP gene variants arose, they had to remove the milk’s lactose through fermentation and at the same time lose 20–50% of its calories. In situations of sporadic famines, those additional calories obtained through LP could aid tremendously in survival and reproduction. This appears to not be coincidental, as lactase persistence can be evolutionarily advantageous.6

C Evolutionary/Environmental Adaptation to Dietary Sugars

The ability to digest the milk disaccharide lactose declines after weaning in most mammals. In certain human populations that do not consume dairy products, intestinal lactase (lactase-phlorizin hydrolase) activity decreases during the first 4 years of life to 10% of its original level.36 Furthermore, as revealed by epidemiological studies, the remaining levels of disaccharidase activity in lactose-intolerant subjects vary among ethnic groups.37 Lactose intolerance is a common condition for more than half of adult humans, but it differs from congenital lactase deficiency (MIM #223000), which is a rare and severe gastrointestinal disorder.37

However, in human populations that consume fresh milk and dairy products, lactase persistence allows adult subjects to digest lactose. The shift from lactose intolerance to lactase persistence constitutes an elegant example of evolutionary adaptation discovered by combining epidemiological and archaeological approaches.

Lactose intolerance is a recessive trait, whereas lactase persistence is dominant. The lactase persistence locus is between intron 13 and exon 17 of the minichromosome maintenance complex component 6 gene (MCM6) located upstream of the lactase gene (LCT). The T to C variant at − 3712, together with the European C to T variant at − 13910, shows greater transcription factor (Oct-1) binding than the ancestral variants. When both SNPs are present, the activity of an upstream enhancer of the LCT promoter is elevated and enables persistent lactase production into adulthood.26,38 An evolutionary advantage of lactase persistency could be enhanced calcium absorption, which can prevent osteoporosis.

Symptoms of lactose intolerance are diarrhea, gas bloat, and abdominal pain caused by the fermentation of undigested lactose in the distal intestine, but these symptoms do not appear in all lactose malabsorbers. The diagnosis of lactase intolerance is confirmed by a hydrogen breath test after lactose absorption or by genetic analysis. Eliminating all lactose sources from the diet is not recommended; rather, the quantity of lactose in milk, ice cream, cheese, yogurt, etc., that can be supported by the subject must be determined by personal experience.

a Lactase genes

The ability to digest the sugar lactose, the main carbohydrate found in milk, is governed by the production of lactase, an enzyme that, for most of the world's populations, declines after weaning. This ability to cleave lactose into its constituent monosaccharides, glucose and galactose, is essential for newborn mammals whose sole source of water and nutrition is milk; the inability to do so leads to abdominal pain and diarrhea. However, following weaning, the production of lactase declines significantly in mammals, including some humans.

The persistence of lactase production is thought to have been an example of the coevolution of genes and culture. Common in Europe and in many pastoralist groups in Africa, the Middle East, and Asia, lactase persistence (LP) is thought to be of evolutionary significance in relation to cattle domestication and the increase of dairying. It is thought that this trait has been subject to strong selective pressures, as the ability to digest lactose in adulthood would confer an advantage due to the increased nutritional benefits of being able to drink milk, as well as it being a source of water. Genetic analyzes of this trait in modern populations in Europe, Africa, and the Near/Middle East suggest that at least four SNPs (autosomal dominant) within the MCM6 gene (found upstream in the promoter region of the lactase gene) are thought to be associated with LP. The geographical spread of these SNPs suggests that at least two, and probably four or more variants that are associated with LP (Table 5), have arisen separately.

Table 5. SNP Variants of Lactase Genes

Information taken from Itan, Y., et al. (2009). The origins of lactase persistence in Europe. PLoS Computational Biology, 5(8), e1000491 and Tishkoff, S. A., et al. (2007). Convergent adaptation of human lactase persistence in Africa and Europe. Nature Genetics, 39(1), 31–40.

Age estimates for these alleles are consistent with a correlation between LP and the rise of the practice of pastoralism. The allele which has been the focus of most analyses is the − 13,910C > T transition in Europe; this allele has apparently been under strong selective pressure from < 10,000 years ago, coinciding with the rise of domestication and dairying during the Neolithic (Fortes et al., 2013). A comparison of the genetic–phenotypic profiles between Kazakh (traditionally herders) and Tajiko-Uzbek (agriculturalist) populations in Central Asia has shown a significant difference of this polymorphism between the two populations, together with an expansion of the − 13.910*T around 6000 and 10,000 years ago (Heyer et al., 2011). It has also been found in India and West Africa (Priehodová et al., 2014). Other alleles associated with LP appear to have arisen independently: − 13,915G in Arabia, and − 13,907G and − 14,010C in Africa, with some in Africa carrying the − 13,915G allele as the result of the spread of nomadic populations from Arabia to Africa from the sixth century onwards (Priehodová et al., 2014). Other regions are not studied in-depth, so additional alleles or frequencies of existing alleles may be found to be at appreciable frequencies. The ease of assaying the -13.910*T SNP has allowed the evolution and spread of this haplotype, that is so prevalent today, to be tested directly. The allele which confers LP is absent or at low frequencies in Early and Middle Neolithic samples, ranging from as low as 0% in a Mesolithic sample and Early Neolithic samples (Burger et al., 2007; Lacan et al., 2011a, 2011b; Nagy et al., 2011), to 5% in Middle Neolithic sites on Gotland (Malmström et al., 2010), to 27% in Late Neolithic Basque country samples (Plantinga et al., 2012).

43.3.2.4 Dietary Factors in Population Diversity and Evolution

Natural selection and random genetic drift are two factors that may affect allele frequency in a population. Both may lead to the elimination or the preferential selection of a particular allele. Evolution of the LCT gene in world populations, and especially in Africans, has been well documented [37]. This gene is the determinant of the trait commonly called lactase persistence/nonpersistence, depending on whether lactase activity continues from childhood into adulthood.

Populations in various parts of Africa began domesticating animals as a source of food and for ploughing more than 7500–9000 years ago in southern Egypt [38,39]. The foundation of the selection based on LCT variation is that individuals raised in areas where dairying is commonly practiced maintain lactase activity into adulthood while individuals in areas where there is less dairying become lactase nonpersistent as adults. Tishkoff and colleagues [37] looked at the convergent adaptation of human lactase persistence in Africa and Europe and found that the frequency of lactase persistence was lowest in the Khoisan-speaking Sandawe hunter-gatherer population from Tanzania (26%).

In our genome-wide genotyping study [34], among the most highly differentiated SNPs, rs12472293, rs1050115, and rs961360 were found in the surrounding area (within 250 kb) of an LD block containing LCT and the minichromosome maintenance gene 6 (MCM6). We observed that the Kenya Kikuyu (KNK) and the Nigeria Hausa (NGH) maintain minor allele frequencies (MAFs) for all three SNPs in the LCT gene at ∼30%. On the other hand, the MAFs in the San population were observed to be less than 20%.

Genetic variation has also been shown to occur in genes coding for proteins important in disease susceptibility. Such variation has been associated with selection of certain genotypes that confer resistance to some infections. In Africa, important susceptibility and/or resistance genes have been documented for HIV/AIDS, tuberculosis, and malaria.

The next section focuses on pharmacogenomics, which is the study of genetic variation in genes that influence drug disposition and efficacy, and its implications for stratified medicine.

A Adaptation to Dairy Farming

The development of agriculture is hypothesized to have radically altered the dietary habits of modern humans. Cattle raising and dairy farming are important examples of agricultural development, which dates back to Europe about 9000 years ago.78 Lifelong consumption of dairy products requires the ability to digest lactose in milk. This capability varies dramatically, with most Europeans demonstrating lactase persistence (see also Chapter 5). The distribution of lactase persistence is consistent with the dairy farming history.79,80 Using the long-range haplotype method,52 Bersaglieri et al.81 showed that the lactase (LCT) gene has been subject to strong positive selection in European ancestral populations. This is a classic example of strong selection that facilitated dietary adaptation in humans. Other studies53,82 further confirmed that LCT was subject to positive selection in European groups. In contrast, the LCT gene was not under positive selection in Asian populations, in which the lactase-persistence 13910T allele is absent or present at low frequencies.81 In addition, three additional LCT variants detected in east Africans confer lactose tolerance independently of those variants occurring in Europeans. These promoter variants emerged in response to selection sweep (see Fig. 2; an extreme selection leads to 100% of the relevant allele) and represent an example of convergent adaptation.83 On the other hand, these LCT variants also are present at very low frequencies or do not exist at all in East Asian groups. Nucleotide-binding oligomerization domain containing 2 (NOD2) gene variants that are associated with Crohn's disease are present at high frequencies in populations of European ancestry and are likely the result of positive selection that confers resistance against bacteria that may be present in cow's milk.84

Using the iHS method, Voight et al.53 identified a small set of genes (including LCT) that are under positive selection and likely involved in dietary adaptation in different populations. Hancock et al.57 identified two genes (tenascin XB [TNXB] and activating transcription factor 6 beta [ATF6B, also known as CREBL1]) that are subject to climatic selection and are correlated with consumption of fat, meat, or milk.

Historic and Geographic Perspective on LI

The people with a low prevalence of lactose maldigestion (northwest Europeans and certain East African pastoral groups) have long traditions of consuming milk, much of it in lactose-rich forms. This suggests a geographic or cultural-historical hypothesis based on the assumption that in the hunting-and-gathering stage, human groups everywhere were like most other land mammals in their patterns of lactase activity. That is, in the normal individual, lactase activity would drop at weaning to low levels, which prevailed throughout life. With the beginning of dairy farming, however, significant changes occurred in the diets of many human groups. As a result, there may have been a selective advantage for those aberrant individuals who experienced high levels of intestinal lactase throughout life. In classic evolutionary terms, the condition of high intestinal lactase activity throughout life, or lactase persistence, would come to be typical of such a group.

Children of some ethnic groups (e.g., Thai) commonly lose lactase at 1–2 years of age while in others (e.g., Finns) lactase persists until later in life (10–20 years of age). According to some estimates, approximately 70% of the world's population has primary lactase deficiency. The frequency of lactose maldigestion varies widely among populations but is high in nearly all but those of Northern European origin.

Lactase deficiency in Europe has been reported to vary between 4% (in Denmark and Ireland) and 56% (in Italy). In South America, Africa, and Asia, more than 50% of the population is reported to have LNP, and, in some Asian countries, this rate is almost 100%. A study of gene-identified LI in a Dutch Caucasian elderly population is associated with lower dietary calcium intake and serum calcium levels but is not associated with bone mineral density or fractures. The paradox reinforces the complexity of the disease and the importance of biologic, genetic, and as yet undetermined factors in the etiology of osteoporosis. The lactase persistence trait is more common in populations that practice cattle herding and dairy farming, and it is related to genetic selection of individuals with the ability to digest lactose.