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So, in my world (or more rather the region in which my story takes place) when the nuclear war happened the majority of people survived in small, survivalist compounds, remote wilderness shelters, and underground bunkers. All in all, 20,000 people survived the war.
I wanted to use the Founder’s Effect, that genetic thing, to make the majority of people in the surviving communities colorblind. My question is, can the founders Effect make this happen?
Yes. This happened on a small Pacific island with a population bottleneck after a typhoon.
https://en.wikipedia.org/wiki/Pingelap
Complete achromatopsia is normally a very rare condition, and its prevalence on the island has been traced back to a population bottleneck in 1775 after a catastrophic typhoon swept through the island, leaving only about 20 survivors. One of these, Doahkaesa Mwanenihsed (the ruler at that time), is now believed to have been a carrier for the underlying genetic condition, but the achromatopsia disorder did not appear until the fourth generation after the typhoon, by which time 2.7% of the Pingelapese were affected. Since achromatopsia is an autosomal recessive disorder, inbreeding between the descendants of Doahkaesa Mwanenised would result in an increased recessive allele frequency.[8] By generation six, the incidence rose to approximately 4.9%,[7] due to the founder effect and inbreeding, with all achromats on the island nowadays tracing their ancestry to Doahkaesa Mwanenihsed.
Today the atoll is still of particular interest to geneticists; due to the small gene pool and rapid population growth, the disorder is now prevalent in almost 10% of the population...
The same thing can happen in your post apocalyptic world. After a population crash (bottleneck) the founder effect leads to this and possibly other genes being represented at a markedly higher frequency. If I recall, you considered having reduced fertility among survivors. If there were a man back in the day who had a reputation as a baby maker, most or all of the survivors might trace their ancestry to him.
Comments by @Mary is right. 20K is too many for the founder effect. I thought that 20K was the population rebounded some generations after the apocalypse and bottleneck. But you could have the founder effect responsible for colorblindness going into the apocalypse. Maybe there is a Doomsday cult that started with a charismatic leader back in the 1800s. Many of the current cult members are descended from that leader and his many wives. It turns out their preparation served them well, because the cult represents a large proportion of those surviving the apocalypse.
Twenty thousand people is an enormously large population to have a big Founder Effect. To produce this you would need:
One possibility would be that for some reason, ability to see through camouflage is immensely important; colorblindness helps with that.
Still, the sort of flukes that would get it started are much more likely to occur in maybe one or two small communities, and its spreading would turn on other communities be wiped out for the lack.
Your problem for limiting genetic diversity is that you have too many "breeding pairs" to get any significant genetic diversity. You need some way to limit that. The obvious way is to limit which men breed., or that you simply (for whatever reason) don't have that many men.
Your survivors were a girl guide jamboree. The vast majority naturally were female, with one or two male site assistants. I have trouble imagining another context for the survivors being overwhelmingly female though, but this is kind of vaguely possible.
Your survivors were fairly evenly gender-balanced, but the effects of near-extinction killed male fertility. After 10 years of no pregnancies, the doctor screened sperm samples for all men, and found only one guy with properly viable sperm. He became the sperm donor for refounding the world. They could easily manage artificial insemination to increase reproduction - that's low tech with a turkey baster - but they wouldn't have the ability to gene-edit to fix anything wrong with his chromosomes.
I suggest going with the founder effect, as described in Willk's answer, combined with a political effect.
At first the colour blindness is just present in the leader and their family. They tend to get more children than other people making the gene more common.
Later anybody who claim to see these "colours" will be executed as this is an implication that the First Family is less then perfect.
Eventually the few remaining people who are not colour blind have learned to shut up about it.
Color vision is so vital to human survival that it would be difficult to explain this with only genetics. Red-green colorblindness is sex linked so it may be possible to explain a prevalence of red-green colorblindness after a war by explaining that men with good color vision went off to war and died, leaving noncombat military and those unfit for service behind to have children.
Blue-yellow colorblindness is rare as there are redundant genes for this, it would take quite a bit more effort to remove the blue receptor gene from the gene pool.
Blue-yellow colorblindness can be acquired from overexposure to UV light. Even cheap sunglasses will have a UV protective coating, and many kinds of glass (like the thick glass used on high rise buildings and in car windshields) naturally filter out UV. In a society that has had scarcity caused by war there may be people using lighting that produces a lot of UV, and people in dimly lit places will not be wearing sunglasses. This can have a genetic component in that some people have more natural protection against UV than others. Lights that produce UV are fluorescent lights, arc lamps, and various gas/vapor lamps. Mass produced lights of this kind will have UV filters but those improvised after a war might not.
Diseases like diabetes can cause colorblindness if not managed well. This has a genetic component as people can present inherited diabetes at a young age, or acquire it from a combination of bad diet and genetics for poor metabolism over time.
Vitamin A deficiency can cause colorblindness if allowed to last long enough. This is unfortunately quite common with children receiving poor diets. This can have a genetic component as some people absorb and process vitamin A more readily.
Some drugs can cause colorblindness. In a war torn society it's easy to choose a near certainty of color blindness over near certainty of death from some disease. A common tuberculosis treatment was known to cause colorblindness as an example.
I'd "stack" the causes of colorblindness to explain it's prevalence. Bad diet, bad lighting, and less than desirable treatments for disease leaves everyone colorblind before they become an adult. Add in genetics from many healthier people in the population going off to die in war makes them more vulnerable to such causes.
A different kind of founder effect - disease:
There are a multitude of diseases in the world, and viruses can cause some pretty unique ones. In conditions with poor healthcare, a minor virus no one ever noticed can become a huge public health problem. Polio was a significant virus mostly because changes in health standards meant people started catching it during a time in life where its side effects were most severe.
If ONE of your survivors had a virus that, in poor health conditions and sanitation, could infect the majority of your survivors and circulate in the population, you have a vector to cause any disability you want. Let's say your virus infected small infants during eye development and caused a defect in cones. No one noticed the virus before because it was rare, and good healthcare meant children rarely caught it. In an adult, it would be like a cold. Well-meaning survivors giving vital supplies to fellow survivors unwittingly have caused a new epidemic.
Your population wouldn't probably even understand why so many people were colorblind - the disease might not even cause any symptoms detectable in a baby. The great thing about this is that you can have it be as mild or severe as you want - some people might only have partial effects, others miss only certain colors, and a few rare people would have destroyed foveas and serious vision problems. The details are up to you, and wouldn't need to run in families (although they could, there can be sensitivities, or the disease can be hard to transmit without close contact).
The virus could also be neurological, affecting the parts of the brain that interpret color. For this, the virus could even affect adults - one day you're fine, then you catch a cold, and a week later you have red-green color blindness.
If you want to be poetic, make it a prion passed in tears - the sorrows of your survivors caused its spread.
