Many variants, such as the millions of mobile element insertions (MEIs), exist at a very high frequency with the majority become fixed in the human populations. Since the presence of MEIs happens as identical by ancestry, for a MEI to be fixed or reach a high frequency in a very large population starting from a single individual can only be achieved by graduate increase of the MEI allele overtime. Is it safe to conclude that all fixed or high frequency MEIs in human populations were subject to positive selection?
@Saul is correct. It may be in a high frequency because it's neutral or nearly neutral and there's no fitness costs associated with it that could purge it from the population. If it's a small population or a population with a small effective population size, then drift dominates and these types of alleles can quickly move towards fixation.
Thank you, Dave, although I was talking about the large number of MEIs that are fixed in the entire human populations, among which many are human-specific. So I guess if drift was responsible, then these insertion events had to occur when the ancestral population was very small or there was a very severe bottleneck to all humans post these insertion events.
Piang, I see your point, and I think you're right. Perhaps, though, these MEI's can be considered alleles (I always have to remind myself that an allele is not always considered just a single nucleotide), and yes, perhaps the original human population was small or was bottlenecked. It'll be very interesting to learn about what you discover with these MEIs
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