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I read in this question that the minimum viable population without causing large problems in genetic diversity is about 50. If we have a larger population (say a hundred) and genetic diversity becomes a problem and the effects of incest kick in, the population is not guaranteed to go extinct. This will mean that genetic problems will be inherited by most of the population very quickly. Assuming the population survives, how long will it take for this relatively monogamous society to regain the modern genetic diversity of modern America?

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  • $\begingroup$ Are you interested in how long it takes to restore thousands of years and millions of people's worth of variation, or how long it takes for the population to become reasonably free of inbreeding issues? The question states the former, but from your description it seems you may be interested in the latter. $\endgroup$ – Mike Nichols Jun 22 '15 at 23:08
  • $\begingroup$ I want how long it will take to get something rrecognizably close to todays genetic diversity and no issues. Basically something in between, but you can opt for the latter if you need. $\endgroup$ – JDSweetBeat Jun 22 '15 at 23:10
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First off, I know you didn’t ask for a genetics lesson, but I need to explain some fundamentals. The majority of human variation occurs in the form of Single Nucleotide Polymorphisms or SNPs. A SNP is a difference in one nucleotide base of the DNA molecule. So if some people have a cytosine base at position 1,000,000 on Chromosome 1, and others have a thymine base, then the 1 millionth base on chromosome 1 is a SNP. According to wikipedia it is estimated that there are anywhere from 10 million to 30 million SNPs in the human population. This number only includes those polymorphisms which occur at at least 1% frequency in the human population, so it ignores very rare variation. The human genome has a of total of ~3 billion bases across its 24 unique chromosomes. This means that 1 out of every 100 to 300 bases in the genome is a SNP. Now, any 2 people will have the vast majority of these SNPs in common. If 2 people differed at all 30 million of them, their genomes would only be 99% similar.

On to the question at hand. Let's estimate how much of this starting variation the founder population of 100 will have. Each will bring 2 copies of the genome, so we start with a total of 200 copies of every base in our starting gene pool. I said before that each of these 30 million SNPs occurs at at least 1% frequency in the population. So each of our 200 copies of each base has at worst a 1% chance of having the less frequent variant. This means that the probability of any given SNP in the general human population having copies of both alleles in our founding population is at least ~87% (according to a binomial calculator I found online). If the frequency of the less common allele is higher than 1%, then that chance increases, so 87% is the worst case for capturing the rarest SNPs. Many SNPs will have frequencies closer to 50/50, in which case the chance of getting copies of both is nearly 100%. I would therefore estimate that ~90% of SNPs, which make up the majority of human genetic variation will be maintained in our founder population, assuming they were as genetically diverse as possible. That means we might lose 10%, or 3 million rare SNPs. Additionally, in the first few generations of the population more variation could be lost through random chance, but this could be minimized as long as the founders have lots of children. The total loss of genetic diversity probably won’t be a big deal, but in case you want to recoup those losses the wikipedia article I linked earlier estimated that 60 new mutations occur in every new human we make. To get 3 million new mutations we would need 50 thousand new humans. Again, some of those mutations will be lost randomly, but I think its a reasonable estimate.

Some caveats to this are that I am only considering Single Nucleotide Polymorphisms. There are also copy number variants and other larger features that vary between individuals, but there are far fewer of these than there are SNPs. I’m also only considering polymorphisms that occur at at least a 1% frequency, anything super rare is fairly likely to get lost, but the rare stuff will also be the first to come back with new mutations. Also, we are only considering the autosomes here. There will only be 150 X chromosomes in the starting population and only 50 Y chromosomes. The Y will lose a large percentage of its rare variants, but considering half the population does just fine without a Y it shouldn't be too bad.

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  • $\begingroup$ So the basis of your answer is that th chances are in favor of the starting population having alot of diversity and that even though some genes will surely be lost this can be downplayed by cranking out kids in the dozen? For the record I love genetics, so a "lesson " is fine ;) $\endgroup$ – JDSweetBeat Jun 23 '15 at 12:48
  • $\begingroup$ @DJMethaneMan Yes, I'm saying a founding population of 100 will capture the majority of all genetic variation occurring at a greater than 1% frequency in the population. Be careful when you say genes though. No genes will be lost, only single base mutations. $\endgroup$ – Mike Nichols Jun 23 '15 at 13:15
  • $\begingroup$ I'm not sure if I followed this wall of text to the last so I have to ask: Do you assume that the 100 people are specificly chosen from all over the world with this in mind? Because the linked question asks about random persons - not perfectly diverse people - and OP didn't specify. The most likely constellation of people forming a separat/ last society that lives long enought to reproduce would be members of the same people or tribe (same cultire, sence of unity but bad gene diversity). If we are lucky they are from America or Australia but even than they might not be very diverse. $\endgroup$ – hajef Jul 25 at 8:06
  • $\begingroup$ @hajef The takeaway from my answer is that 100 people is enough of a starting group that the majority of all of the genetic diversity within the population that starting group is drawn from will be maintained. If the starting population has lots of diversity then so will the 100 survivors, but if all of the starting population come from a single race, then, of course, the survivors will all share certain characteristics. The point though is that they will have plenty of genetic diversity to not suffer any ill effects from a reduced population size, assuming their population subsequently grows. $\endgroup$ – Mike Nichols Jul 26 at 14:46
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Assuming

  1. A founder population of 100 people (50 men and 50 women) with no fore-bearers in common going back at least 5 generations.
  2. Five children per couple per generation.
  3. Good records are kept and laws are enforced which forbid intermarriage/procreation with someone who you are related to for as many generations as possible.
  4. The founder population is as genetically diverse as possible (per Mike Nichols SNP discussion).

Then

  1. Given the assumptions, at generation 0 your population is already likely more genetically diverse than the present US. This seems counter-intuitive, because the US has a high degree of cultural and racial diversity, and a large population, nearly all immigrants within the last 200 years from all corners of the globe. It is important to recognize that 'culture' and 'race' are social constructs, and genetic diversity is a crisply quantifiable scientific quality. In the Wikipedia article quoted by Mike Nichols, the greatest amount of genetic diversity occurs among and within populations in Africa, and is reduced in the migratory distance from Africa, with Europeans being less genetically diverse than Africans, and Asians being less genetically diverse than Europeans, with aboriginal North-and-South Americans being even less genetically diverse. Most African-Americans originated in West Africa, somewhat distant from the most genetically diverse section of Africa (Southern) and represent about 13% of the current population of the US.
  2. At generation 4 >50,000 new humans have been added and the lost 10% genetic diversity from gen0 is likely restored, though it is highly likely that the 'new' diversity is very different from the 'old' diversity.
  3. Somewhere after gen9 you have more people than the present US.
  4. Somewhere after gen11 you have more people than are currently on Earth.
  5. Around gen6, the laws will need to permit people to marry even if they are related at Gen 0. However as the population has grown from 100 to about 1.6 million, with a total of 1.9 million new people added, and with 3 million SNP mutations per 50,000 people, about 1.7 million new (possibly overlapping) mutations have occurred.
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I would say, how long did it take the first time? I would guess it would take just as long again. It is believed we almost went extinct about 70,000 years ago, and we were reduced to approximately 3000 individuals, so I'd say between 70,000-80,000 years if it was mostly natural mutations.

Edit: If the survivors know enough about genetics and can put together a plan to get a none threatened population level up, then things could be a bit faster. Having different parents for each child is one way to speed things up and create a stronger gene base. Good records would have to be kept for several generations, if not more to try and prevent incestuous relationships that could be damaging. People would actually be the opposite of 'horny teenagers' because they likely wouldn't be picking their own sexual partners, at least not for purposes of procreation. this might bring the total time down by more than half, depending on how long the 'plan' is followed (honestly, likely much less than the first 1000 years following a 'plan')

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  • $\begingroup$ I thought there might be some reason I did not take into account that it could happen sooner. $\endgroup$ – JDSweetBeat Jun 22 '15 at 17:44
  • $\begingroup$ @DJMethaneMan There always COULD be something that might make it happen faster or slower, but I would tend to stick with what has actually happened. I just noticed you put in monogamous as well. That I suspect would actually slow things down, not speed them up. $\endgroup$ – bowlturner Jun 22 '15 at 17:47
  • $\begingroup$ Well....I am looking for a timeframe and a way that would not involve 99% of the population acting like horny teenagers (lol because I am one). $\endgroup$ – JDSweetBeat Jun 22 '15 at 17:52
  • $\begingroup$ @DJMethaneMan Well, intelligent breeding, by having children by multiple fathers would spread the genetic diversity around the most. Planned parentage to maximize things would be the 'safest' and fastest way to get to a 'safe' and stable genetic base. The better the original mix of survivors and the better the planning, could reduce the 'diversity' problems down by 10's of thousands of years. $\endgroup$ – bowlturner Jun 22 '15 at 17:56
  • $\begingroup$ @DJMethaneMan added more to my answer. $\endgroup$ – bowlturner Jun 22 '15 at 18:03
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Over short periods of time, your population's genetic diversity can only decrease. Diversity for this population can only increase by the introduction of new gene alleles (usually due to mutation). To gain diversity, you need to do one of the following:

  1. expose the population to conditions with high selective pressures (aka a high death rate)
  2. increase the mutation rate (aka a high death rate)
  3. use genetic engineering to artificially create more diversity
  4. or some combination of the above

Before pursuing either 1 or 2 you ought to get your population higher to ensure survival of the species first.

Unfortunately, this two step approach (increase population first and then increase the mutation rate) and the fact that I don't know how drastic you're willing to be about them means that I can't provide a quantitative answer.

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    $\begingroup$ I will be as drastic as required.... $\endgroup$ – JDSweetBeat Jun 22 '15 at 14:07
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    $\begingroup$ Your first point is wrong, Selective pressure does not cause mutations. It only acts on what diversity already exists. Shrinking your population can only decrease genetic diversity. If you mean that the selective pressure will purge negative alleles from the population, then that is still decreasing genetic diversity. $\endgroup$ – Mike Nichols Jun 22 '15 at 14:23
  • $\begingroup$ Not wrong, merely stated unclearly. Selection pressures (can) drive genetic diversion. Mutations introduce the change, selection pressures select the successful changes. Strong selective pressures increase the rate at which the mutations "fix" in the population. I'll look at rewording the answer to clarify. $\endgroup$ – Jim2B Jun 22 '15 at 14:34
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    $\begingroup$ To have a high mutation rate all that you need is a lot of descendents; each new baby born is a possibility for the introduction of new mutations. High selective pressure may be needed if the situation is that of a stable, well stablished species; but a new species that gets to spread does not need that to begin increasing its variability. $\endgroup$ – SJuan76 Jun 22 '15 at 15:15
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    $\begingroup$ Right, but my method attempts to "fix" new genes into the population to increase genetic diversity. You might not expose the whole population to radiation and challenge environments (in fact this could be a very dramatic tension point) but by keeping the original populations fixed genes stable and then introducing environments to subsets of the population, you drive that group to a different local optima - you increase the overall gene set which increases diversity. $\endgroup$ – Jim2B Jun 22 '15 at 17:11

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