11. Population and evolution genetics
11.2. Evolutionary genetics
usually 0.05. When the null hypothesis is rejected (p<0.05), the result is said to be statistically significant.
In retrospective studies the odds ratio (OR) is used for the estimation of the risk.
This value has a direct connection with the p-value. The odds ratio is the ratio of the odds of the association of an allele with the trait (disease) in cases to the odds of it in the control group.
In prospective studies and in clinical trials the relative risk (RR) is used. Relative risk is a ratio of the probability of the association in the case group versus a control group.
If these values are greater than 1, then the risk is elevated, if they are <1, it is lower.
Next to these values, their 95% confidence intervals (95%CI) must be given, which depends mainly on the population size. The larger the population, the narrower the 95%CI is. For statistically significant association both values of the 95%CI must be above 1, if the OR, or RR is >1, and below 1, if these values <1. E.g. OR = 2.2 (95%CI 1.3-3.9) is significant, OR = 2.2 (95%CI 0.9-4.5) is not significant. If the p-value < 0.05, then the OR is significant.
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evolution of more diversity and complexity, but it has also made humans more reliant on the innovations that freed them from selection.
11.2.1.2. Role of infections in formation of the genome
The different microorganisms and infections have one of the largest roles in the formation of human genome. This selection factor played even important role in the history of the modern human (see e.g. Population history of indigenous peoples of the Americas), and its effect can be felt even today. Think about the large epidemics like cholera, pest, influenza, pox, TBC, etc., which frequently decimated the population.
Individuals who contracted one of these infections often died and were not able to pass their genome to the next generation. In contrast, there were individuals who were resistant or survived and could pass their genomes which gave them greater fitness. The today population is the descendant of those who survived all the infections, and were able to pass their genome to the next generation. Naturally, not only the genome influences how individuals respond to an infection, but several other factors as well, like the actual physical state, other infections, age, epigenetic states, pure chance, etc.
During the last years several traces of these microorganism–human genome interactions could be detected in the human genome. E.g.:
Several hundreds of human genes originate from bacteria, through horizontal gene transfer.
8% of our genome originates from retroviruses. These two points are examples of gene flow.
There are human genes specifically against bacterial or viral infections, like genes for pattern recognition receptors like TLRs, MBL, CD14, NOD2 etc., or for antiviral proteins like APOBC3G, TRIM5, BST2.
The microorganisms render selection pressure on human genome even today. In a GWAS carried out in 52 populations, 441 variants mapped to 139 human genes were identified significantly associated with virus-diversity. Analysis of functional relationships among genes subjected to virus-driven selective pressure identified a complex network enriched in viral products-interacting proteins.
11.2.1.3. Genetic drift
The genetic composition of a population is also influenced by random effects. Such an effect is e.g. when a small group in a population splinters off from the original population and forms a new one. The random sample of alleles in the just formed new colony is expected to grossly misrepresent the original population in at least some respects. It is even possible that the number of alleles for some genes in the original population is larger than the number of gene copies in the founders, making complete representation impossible. When a newly formed colony is small, its founders can strongly affect the population's genetic make-up far into the future. This is a type of the bottleneck effect.
Another random event can be, when an individual (e.g. a king) has disproportionately more descendants than others in a small population, and his alleles become more frequent, or a war, or a natural disaster kill the majority of the population.
This is called genetic drift and is different from the natural selection.
The genetic drift can have medical consequences, when an allele which became widespread in an environment, but can make susceptibility to a disease in another.
From evolutionary genetic point of view population genetics is the study of allele frequency distribution and change under the influence of the evolutionary processes:
natural selection, genetic drift, mutation and gene flow.
11.2.2. Why are some lethal mutations frequent?
According to the Darwinian Theory and logic, the frequencies of deleterious mutations or mutations which produce organisms of lower fitness should decrease from generation to generation. But some deleterious mutations causing serious diseases are very frequent in certain populations. How is it possible?
The explanation is the balancing selection, or heterozygote advantage, which describes the case in which the heterozygote genotype has a higher relative fitness than either the homozygote dominant or homozygote recessive genotype. Polymorphism can be maintained by selection favoring the heterozygote, and this mechanism is used to explain the occurrence of some kinds of genetic variability. A common example is the case where the heterozygote conveys both advantages and disadvantages, while both homozygotes convey a disadvantage.
One of the most well-known examples in the Caucasian population is the cystic fibrosis. This is the most common autosomal recessive genetic disorder. Its population frequency is 1/2500-3000, and the prevalence of mutation carriers is 1/28. CF is caused by a mutation in the gene for the protein cystic fibrosis transmembrane conductance regulator (CFTR). This protein is required to regulate the components of sweat, digestive juices, and mucus. CFTR regulates the movement of chloride and sodium ions across epithelial membranes, such as the alveolar epithelia located in the lungs.
Although most people without CF have two working copies of the CFTR gene, only one is needed to prevent cystic fibrosis due to the disorder's recessive nature.
The ∆F508 mutation (deletion of 3 bases from the gene, causing deletion of the phenylalanine 508 from the protein), is the most frequent cause of the disease, the majority of the affected carries this mutation. The symptoms are very serious already in early childhood. In 1959, the median age of survival of children with cystic fibrosis in the USA was six months. The survival time improved significantly, but males are often infertile due to congenital absence of the vas deferens. Thus, it is exactly the disease type, in which the mutation is lethal and according to the natural selection the frequency of the mutation should be lowered from generation to generation.
The ΔF508 mutation is estimated to be up to 52,000 years old. Numerous hypotheses have been advanced as to why such a lethal mutation has persisted and spread in the human population. The following hypotheses have been proposed as possible sources of heterozygote advantage (Wikipedia):
• Cholera: With the discovery that cholera toxin requires normal host CFTR proteins to function properly, it was hypothesized that carriers of mutant CFTR genes benefited from resistance to cholera and other causes of diarrhea.
• Typhoid: Normal CFTR proteins are also essential for the entry of Salmonella Typhi into cells, suggesting that carriers of mutant CFTR genes might be resistant to typhoid fever. No in vivo study has yet confirmed this. In both cases, the low level of cystic fibrosis outside of Europe, in places where both cholera and typhoid fever are endemic, is not immediately explicable.
• Diarrhea: It has also been hypothesized that the prevalence of CF in Europe might be connected with the development of cattle domestication. In this hypothesis,
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carriers of a single mutant CFTR chromosome had some protection from diarrhea caused by lactose intolerance, prior to the appearance of the mutations that created lactose tolerance.
• Tuberculosis: Another possible explanation is that carriers of the gene could have some resistance to TB.
The heterozygote advantage is easier to be explained in sickle cell anemia. This is also an autosomal recessive disease, which is very frequent in individuals of African origin, especially in people (or their descendants) from parts of tropical and sub-tropical regions where malaria is or was common. In the USA the prevalence of the disease is 1/600 in black, and the frequency of carriers is 1/12. There are certain symptoms, however, even in heterozygotes. Five percent of carriers have blood in their urine, and have symptoms if they are deprived of oxygen (for example, while climbing a mountain).
The main cause of the disease is a mutation in the gene that produces beta-globin, a protein needed to produce normal haemoglobin. This is a Glu6Val mutation and the gene product is called haemoglobin S.
Haemoglobin S (sickle cell trait) provides a survival advantage over people with normal haemoglobin in regions where malaria is endemic. The trait is known to cause significantly fewer deaths due to malaria, especially when Plasmodium falciparum is the causative organism. This is a prime example of natural selection, evident by the fact that the geographical distribution of the gene (for haemoglobin S) and the distribution of malaria in Africa virtually overlap. Because of the unique survival advantage, people with the trait increase in number as more people infected with malaria and having the normal haemoglobin tend to succumb to the complications.
Although the precise mechanism for this phenomenon is not known, several factors are believed to be responsible.
• Infected erythrocytes tend to have lower oxygen tension, because it is significantly reduced by the parasite. This causes sickling of that particular erythrocyte, signalling the phagocytes to get rid of the cell and hence the parasite within.
• Since the sickling of parasite infected cells is higher, these selectively get removed by the reticulo-endothelial system, thus sparing the normal erythrocytes.
• Excessive vacuole formation occurs in those parasites infecting sickle cells.
• Sickle trait erythrocytes produce higher levels of the superoxide anion and hydrogen peroxide than do normal erythrocytes; both are toxic to malarial parasites.
The sickle cell trait was found to be 50% protective against mild clinical malaria, 75% protective against admission to the hospital for malaria, and almost 90% protective against severe or complicated malaria.
Another example of the selection advantage is the frequent CCR5∆32 mutation in the Caucasian population. The CCR5 is a chemokine receptor, and the 32 bp deletion does not cause any significant symptoms in humans, although the resulted protein product is functionless. But, as CCR5 is an essential co-receptor for the HIV-1 to enter
the cells, the lack of it protects individuals from the infection. In the European population the frequency of the ∆32 mutation is very high, 1/100 individuals homozygote for it, and thus protected from HIV-1 and AIDS. Even heterozygotes have some advantage. Although they can be infected by the virus, but the AIDS disease developed significantly slower in them (2-4 vs. 6-8 years, in untreated people).
Interestingly, the mutation occurs only in people with European ancestry. According to researches the mutation appeared 7000 (2900-15750) years ago. Possibly there was an epidemic at that time in this population, in which the pathogen used the same receptor for the infection. So far, this infection has not yet been identified, but there are some suspects like pest and pox. In 2012 it was identified the CCR5 as a cellular determinant required for cytotoxic targeting of subsets of myeloid cells and T lymphocytes by the Staphylococcus aureus leukotoxin ED (LukED). CCR5-deficient mice are largely resistant to lethal S. aureus infection thus this finding put forth the possibility that resistance to S. aureus leukotoxins may have influenced the selection of the Δ32 allele.
11.2.3. Examples for effects forming the genome
In the last years more and more people have been sequenced in different populations. It gives the possibility to compare their genomes and detect population-specific variations, some of them developed through population-specific gene-environmental interactions.
Let us see some examples!
One of the most marked differences between populations may be the skin color. The environmental factor which induced the differences was the sunlight. Individuals from populations lived in sunny environment have darker skin, those who experienced less sunlight have lighter skin. The main cause of the selection pressure in the sunlight is the UV radiation. It can cause DNA mutations and cancer in the skin (melanoma). The best defense against it is the melanin produced by melanocytes, which gives the skin dark color. The other selection pressure is the D vitamin produced in the skin when exposed to sunlight. But high melanin content decreases this process. Two genes SLC24A5 and SLC45A2 were identified as major determinants of pigmentation in humans and in other vertebrates. The allele A111T in the former gene and the allele L374F in the latter gene are both nearly fixed in light-skinned Europeans, and can therefore be considered ancestry informative marker. An L374F substitution in SLC45A2 was found at 100%
frequency in a European sample, but was absent in Asian and African samples. An association study has shown that the Phenylalanine-encoding allele is correlated with fair skin and non-black hair in Europeans. These data support SLC45A2 as a target of positive selection in Europe.
There are examples even today for the selection pressure of the sunlight. The prevalence of melanoma has been increasing in light-skinned populations due to excess exposure to sunlight (sunbathe), and 100% of black-skinned individuals of African origin, 93% of Indians and 85% of East-Asians living in Canada suffer from D vitamin deficiency.
Available food can also be a selection factor. One example for it is the AMY1 gene coding for salivary amylase, which digests starch. AMY1 is one of the few genes in the human genome that show extensive copy-number variation between individuals. Extra AMY1 copies endow the individuals carrying them with the capacity to produce more salivary amylase. In a study two groups were investigated: one consisted of four populations with a low-starch diet and the other of three populations from agricultural
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societies and hunter–gatherers in arid environments, who traditionally eat high-starch food. Strikingly, twice as many members of the high-starch-diet group had at least six copies of AMY1. This difference could not be explained by geographical factors, because both groups contained people of Asian and African origin. Instead, the authors propose that variations in AMY1 copy number are more likely to have been influenced by positive natural selection. So what is the advantage of having more salivary amylase? Significant digestion of starch occurs during chewing. This is crucial, and probably vital, in people likely to suffer from diarrhoeal diseases. Moreover, after being swallowed, salivary amylase is carried to the stomach and intestines, where it aids other digestive enzymes.
Of the three copies of the AMY1 gene registered in the reference sequence of the human genome, variations in nucleotide sequences are small. This suggests that the duplication of these genes may have occurred relatively recently, possibly even since the evolution of modern humans about 200,000 years ago.
Prehistoric and contemporary human populations living at altitudes of at least 2,500 meters above sea level may provide unique insights into human evolution. Indigenous highlanders living at high altitude have evolved different biological adaptations for surviving in the oxygen-thin air. The Andeans adapted to the thin air by developing an ability to carry more oxygen in each red blood cell by having higher haemoglobin concentrations in their blood. Tibetans compensate for low oxygen content much differently. They increase their oxygen intake by taking more breaths per minute than people who live at sea level. In addition, Tibetans may have a second biological adaptation, which expands their blood vessels, allowing them to deliver oxygen throughout their bodies more effectively than sea-level people do. Tibetans' lungs synthesize larger amounts of nitric oxide from the air they breathe. One effect of nitric oxide is to increase the diameter of blood vessels, which suggests that Tibetans may offset low oxygen content in their blood with increased blood flow.
To pinpoint the genetic variants underlying Tibetans' relatively low haemoglobin levels, researchers collected blood samples from nearly 200 Tibetan villagers living in three regions high in the Himalayas. When they compared the Tibetans' DNA with their lowland counterparts in China, their results pointed to the same culprit — a gene on chromosome 2, called EPAS1, involved in red blood cell production and haemoglobin concentration in the blood. While all humans have the EPAS1 gene, Tibetans carry a special version of the gene. Over evolutionary time individuals who inherited this variant were better able to survive and passed it on to their children, until eventually it became more common in the population as a whole.
Lactose intolerance is the inability to digest lactose, a sugar found in milk and to a lesser extent milk-derived dairy products. Most mammals normally become lactose intolerant after weaning, but some human populations have developed lactase persistence, in which lactase production continues into adulthood. This means that the lactose intolerance may be regarded as the ancient “wild type” phenotype. It is estimated that 75% of adults worldwide show some decrease in lactase activity during adulthood. The frequency of decreased lactase activity ranges from 5% in northern Europe through 71% for Sicily to more than 90% in some African and Asian countries.
This distribution is now thought to have been caused by recent natural selection favoring lactase persistent individuals in cultures that rely on dairy products. While it was first thought that this would mean that populations in Europe, India, and Africa had high frequencies of lactase persistence because of a particular mutation, it has now been shown that lactase persistence is caused by several independently occurring
mutations. These last two examples are examples for convergent evolution, which means that different processes in different population lead to similar phenotypes.
Often, different traits can be developed in individuals, which are only side-effects of the changes induced by natural selection. One of the reasons of this is that most of these genes are pleiotropic: that is, they are individually involved in several different traits.
For example, EDAR regulates hair follicle density and the development of sweat glands and teeth. In humans, selective pressures on EDAR favoring changes in body temperature regulation and hair follicle density in response to colder climates may have influenced tooth shape, although this trait probably does not affect population fitness.
This example shows how 'phenotypic hitchhiking' in genes under positive selection may have substantially increased the observed number of physiological and morphological traits differentiating modern human populations.
Bacteria can acquire mutations or genes which are advantageous for their survival through horizontal gene transfer, e.g. genes for antibiotic resistance. In modern humans it was shown that archaic people contributed more than half of the alleles that code for proteins made by the human leukocyte antigen system (HLA), which helps the immune system to recognize pathogens. Thus, it seems that archaic genome contributed to modern human HLA variations and selection fitness through horizontal gene transfer.