Detecting Positive Natural Selection From Genetic Data

While the human species originated in Africa, when they migrated on to the rest of the world, they were forced to adapt to a whole new way of living.

There were new places to explore, new pathogens that were unveiled and new food sources that had to be discovered. Survival became a completely different way of living.

More recently, there has been a lot of interest in terms of identifying the specific genetic loci within these adaptations that had to be made in order for people to survive the new world. Experts can use whole-genome genotyping and sequencing to look at these factors. 

The different methods for detecting positive selection will work to try and identify alleles that have increased in frequency quickly. The difference between all of the methods used is determined by the information that they use to find the alleles. 

Detecting Positive Natural Selection From Genetic Data

One classification of methods is based on just one assumption, which is if we imagine that selection is acting in one population and not another.

This would suggest that the frequencies of the chosen alleles in the first population would have to increase much quicker than the frequencies of the same alleles in the second population.

This makes the test much simpler; are there actually alleles with larger frequency distances between two populations? Recently, this method was used to identify the gene called EPAS1 as an important factor in terms of adapting to high altitudes in Tibetans.

A class of methods that makes a much different and more restrictive assumption is the one that follows; imagine that selection is acting on a mutation that is new, or at low frequency, in a population.

The selection will also act to increase the frequency of the allele. This would result in a young allele that has a higher frequency in the population. We can actually determine the age of an allele by measuring the amount of genetic variation that surrounds the allele.

The more time that goes by, the more mutations that will have occurred within the region. The age of an allele can also be determined by the length of the haplotypes that the allele sits on.

Similarly in correlation, the more time that goes by, the more that recombination will break up the association of the allele with other alleles that are nearby. The test to do so is also relatively simple and is by finding the young alleles to be at a much higher frequency. 

It can be difficult to avoid explaining these tests without the use of words and knowledge that may require further research to understand, but the methods explained above should be sufficient.

Those who have read and understood these tests will recognize tests that are based on haplotype homozygosity or the site frequency to follow the second method and tests that are based on FST to follow the first method.

There are also different tests that combine aspects from both methods to come to a final conclusion based on their thorough research.