Dennis VenemaFrom Venema at BioLogos:
The key here is that one individual can only have at most two alleles of any gene. A population reduction to one breeding pair would mean that at most, four alleles of a given gene could pass through the bottleneck – in the case where both individuals are heterozygous, and heterozygous for different alleles. The population would then have to wait for new mutation events to produce new alleles of this gene – a process that will take a significant amount of time. Since this would happen to all genes in the genome at the same time – a reduction to a maximum of four alleles – we would notice this effect for a long time thereafter as genetic diversity was slowly rebuilt across the genome as a whole.
So, a bottleneck to two individuals would leave an enduring mark on our genomes – and one part of that mark would be a severe reduction in the number of alleles we have – down to a maximum of four alleles at any given gene. Humans, however, have a large number of alleles for many genes – famously, there are hundreds of alleles for some genes involved in immune system function. These alleles take time to generate, because the mutation rate in humans is very low. This high allele diversity is thus the first indication that we did not pass through a severe population bottleneck, but rather a relatively mild one (estimated, as we have discussed, at about 10,000 individuals by current methods).
Another effect that a bottleneck to two individuals would produce is that there would be no rare alleles after the bottleneck. All alleles would have a frequency of at least 25%. As the population expanded after such an event, those alleles would stay common, and only new mutations would produce less common alleles. What we observe in humans in the present day is that many alleles are rare – even exceedingly rare. The distribution of alleles in present-day humans looks like it comes from an old, large population – not one that passed through an extreme bottleneck within the last few hundred thousand years, which is when our species is found in the fossil record. Thus the observation that we have many alleles of certain genes and the distribution of allele frequencies both support the hypothesis that humans come from a population, rather than a pair. More.
Over to Buggs. This is getting to be fun…
See also: Adam and Eve and the Skeptics, Episode 2: Geneticist Richard Buggs replies
Adam and Eve debut at the Skeptical Zone: In other words, we don’t really know if they could have existed because the human race seems very improbable anyway. But it is high time the question was liberated from the Sunday armchair of theistic evolution, to say nothing of its occasional personal dramas.
Geneticist defends possible Adam and Eve in Nature: Ecology and Evolution
Geneticist: Adam and Eve could have existed