Selection Of Advantageous Variants And Their Influence On Health

Chimpanzees are a close relative to modern humans. A split in the lineage occurred about 5 to 10 million years ago, which was followed by a series of further splits resulting in the emergence of numerous closely related species along the path to the development of modern Homo sapiens.

Using a technique known as immunological distance, scientists were able to verify the timescale of these various splits. This technique relies on the basis that as species diverge, so too do proteins and thus antibody binding for its specific protein will be reduced in different species. Essentially, antibodies produced in species (A) will bind with high affinity to its protein in species (A), but the same antibody will have less affinity for a homologous protein in species (B) because of amino acid substitutions (Barton 2007).

The Time Spans and Relationships of Hominin Species

Before anatomically modern humans appeared, current ‘human traits’ could be observed in several different species over millions of years. Accumulation of these traits eventually evolved to produce the modern H. sapiens of today. For example, Australopithecus was one of the earliest bipedal hominins which have been dated back to between 3 and 4 million years ago.

There are numerous theories as to why this group developed bipedal locomotion, such as to improve hunting or to improve energy efficiency when migrating long distances. A few million years later as the lineage progressed, the discovery of tools alongside skeletal remains dating back 2.5 million years suggested that the genus Homo habilis were the first hominins to make use of complex tools (Barton 2007).

Another human-like trait, whose origin is commonly debated, is the use of fire. Some scientific evidence suggests that Homo erectus were the first to control fire. The use of fire would have enabled H. Erectus to habituate colder climates and therefore advanced the dispersal of hominins around the globe (Coolidge and Wynn 2018).

A schematic tree illustrating four, possibly five gene flow events that have been documented by analysis of the genomes of archaic and present-day humans (Paabo 2014). Archaeologists first identified ‘anatomically modern humans’ shortly after 200,000 years ago, who habituated Africa and the middle east until around 60,000 years ago (Paabo 2014). These modern humans were like present humans, based on their behaviors such as the ability to produce figurative art which was discovered in various caves. They eventually replaced the archaic humans who are extinct hominins that lived during the last 0.5million years, the most notable of the group being Neanderthals. Sequencing of the Neanderthal genome demonstrated that around 2% of genomes in people living all over the world today (except in sub-Saharan Africa) are closely related to the Neanderthals.

Another distant genome that contributes to around 5% of the genomes of present-day people in Papua New Guinea, Australia comes from the Denisovans. Denisovans were a species identified in the Denisovan cave in southern Siberia through genetic analysis of DNA found in a finger bone. The Denisovan genome originated from a common origin of the Neanderthals but had separated early in history (Paabo 2014).

An Italian geneticist Luca-Cavalli-Sforza and others explained that as humans traveled and settled in different locations across the globe, the new populations became isolated from the parent populations, leading to the development of clines as these populations differentiated genetically through adaptions to their new environment (Barton 2007).

Palaeontological and genetics have played an important role in the discovery of the current ‘Out of Africa Model’ which states that Africa is the origin of modern humans, who appeared here approximately 100 to 200 thousand years ago (Reyes-Centeno et al. 2015). It also suggests that all current non-African populations are descendants of the H. sapiens that left Africa at that time. However, this model is much debated in the scientific community (Coolidge and Wynn 2018).

After appearing in Africa, it is hypothesized that modern humans then spread to the rest of the world and eventually replaced the archaic humans (Barton 2007). Modern humans appear to have outcompeted the archaic humans whenever the two crossed paths. Scientists believe this may be due to modern humans being more advanced in elements such as obtaining better communication skills through languages, improved cognitive ability, and larger social groups (Coolidge and Wynn 2018.

Another element which may have contributed to the dominance of modern humans is positive selection. Positive selection occurs in a variety of organisms and arises from changes in the genome (e.g. mutations) that are selected for, in that they benefit those who obtain the mutation (Paabo 2014). Positive selection can benefit the organism in many ways for e.g. increasing survival probabilities in their environment or improvement of fertility (Karlsson et al. 2014).

We can identify genetic variants that have been positively selected for by comparing genome sequences. As humans have evolved over the years, there have been thousands of genetic variations in the genome which has shaped modern humans of today. One example of positive selection taking place is a mutation in an enhancer region of the LCT gene which encodes lactase, an enzyme that breaks down lactose to milk. Transcription of the lactase gene normally ceases after ‘weaning’ in most mammals. However, this is not the case in modern H. sapiens. This comes as a benefit to H. sapiens as it allows for the continuous consumption of dairy products beyond ‘weaning’ without gastrointestinal discomfort. Neanderthals and Denisovans did not carry this mutation (Paabo 2014).

The ability to continue producing lactase is termed ‘lactase persistence’ and is thought to appear more frequent in populations with a history of dairying (Gerbault 2013). The consumption of milk is important for nutrition and may have benefited human ancestors, especially those who practiced dairying in desert regions due to milk satisfying hydration (Scheinfeldt and Tishkoff 2013).

In the past, as humans spread to different parts of the globe, they encountered a variety of different pathogens on their way. Natural selection has played an important role in increasing the prevalence of advantageous variants allowing humans to tolerate diseases caused by these pathogens. A few examples of where positive selection has enabled certain populations of humans to overcome pathogenic diseases include AIDS, Cholera, and Smallpox (Karlsson et al. 2014). Aids is caused by a retrovirus HIV-1 and when it first appeared in the 1980s it killed >30million people. It affects the host by dampening the immune system rendering them highly susceptible to other life-threatening diseases. Differential expression in the MHC loci accounts for 19% of phenotypic variance and is the most plausible explanation of HIV resistance. The protective variant responsible was due to the increased expression of human leukocyte antigen C which prevents the progression of the disorder (Karlsson et al. 2014). Cholera is a deadly disease which has a very high historic mortality rate of 50%. Cholera is induced by the bacterium V. cholerae. A form of positive selection may have occurred in the country of Bangladesh, where there is a high prevalence of Cholera to date.

The positive selection appears to have occurred through blood typing, as the people of Bangladesh have the lowest prevalence of the blood type O. This is beneficial as people with blood type O are more susceptible to a more severe response to the disease. Studies have also indicated cases of genetic cholera resistance. Genetic resistance has developed from genes encoding K+ channels that are involved in cyclic amp mediated chloride secretion and genes which encode components of the immune system which are involved in NFκB signaling. Overexpression of these genes appears to have been positively selected for in the Bangladesh population. (Karlsson et al. 2014). Up until only a century ago, the disease smallpox also had a very high mortality rate of 30%. Smallpox has since been eradicated. However, during the time period when the disease was present, death rates were much lower in Africa (0.4-12%) than elsewhere (4-38%) which suggests some form of positive selection was present in Africa.

Two genome-wide association studies may account for this positive selection. They found that there was an increased amount of single nucleotide polymorphism present in African Americans which are associated with a cytokine response to injection of a smallpox vaccine (Karlsson et al. 2014). Another fascinating example of positive selection is Tibetans adaption to the hypoxic high-altitude environment of the Tibetan plateau where oxygen concentrations are around 40% lower than that of sea level. One may hypothesize that this adaption was achieved through increasing hemoglobin levels, which is the most common method of adaption to hypoxic environments in the average population. However, this is not the case. Genome analysis highlighted numerous genes that play a role in the adaption, with the most notable being the EPAS1 gene which is a transcription factor induced under hypoxic conditions. This gene improves oxygen transport. The source of this adaption is likely to have arisen from the introduction of genetic variants from Denisovan like individuals (Huerta-Sanchez et al. 2014).

In conclusion, it is clear to see that over the years, the human genome has constantly evolved in response to environmental pressures. There is no doubt that as time progresses mutations will continue to occur. However, several scientific papers suggest that humans are no longer dependent on evolution and that humans have instead become dependent on culture and technology to survive (Stock 2008). Stock et al. suggests that we currently live in a prolonged period of environmental stability. One cannot predict when this stability may cease and as a result, we as a species will be forced to undergo adaptions to suit our new environment.

References

1. Barton, N. H. (2007) Evolution, Cold Spring Harbour (N.Y.): Cold Spring Harbour Laboratory Press.
2. Coolidge, F. L., and Wynn, T. G. (2018) The rise of homo sapiens: the evolution of modern thinking, New York, NY: Oxford University Press.
3. Gerbault, P. (2013) The onset of lactase persistence in Europe. Hum Hered, 76(3-4), pp. 154-61.
4. Huerta-Sanchez, E., Jin, X., Asan, Bianba, Z., Peter, B. M., Vinckenbosch, N., Liang, Y., Yi, X., He, M., Somel, M., Ni, P., Wang, B., Ou, X., Huasang, Luosang, J., Cuo, Z. X., Li, K., Gao, G., Yin, Y., Wang, W., Zhang, X., Xu, X., Yang, H., Li, Y., Wang, J., Wang, J. and Nielsen, R. (2014) Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature, 512(7513), pp. 194-7.
5. Karlsson, E. K., Kwiatkowski, D. P. and Sabeti, P. C. (2014) Natural selection and infectious disease in human populations. Nat Rev Genet, 15(6), pp. 379-93.
6. Paabo, S. (2014) The human condition-a molecular approach. Cell, 157(1), pp. 216-26.
7. Reyes-Centeno, H., Hubbe, M., Hanihara, T., Stringer, C. and Harvati, K. (2015) Testing modern human out-of-Africa dispersal models and implications for modern human origins. J Hum Evol, 87, pp. 95-106.
8. Scheinfeldt, L. B. and Tishkoff, S. A. (2013) Recent human adaptation: genomic approaches, interpretation, and insights. Nat Rev Genet, 14(10), pp. 692-702.
9. Stock, J. T. (2008) Are humans still evolving? Technological advances and unique biological characteristics allow us to adapt to environmental stress. Has this stopped genetic evolution? EMBO Rep, 9 Suppl 1, pp. S51-4.