"The extreme population bottleneck that occurred during the biblical Flood should have caused a loss of human genetic
diversity.
According to Scripture, the entire world population was reduced to three reproducing couples.
The maximum effective population size of the Ark-borne population was calculated to be 4.75 individuals (carrying the equivalent of 9.5 haploid genomes).
What effect would this have had on allelic diversity today?
How much ‘created diversity’ would have been lost?
The HapMap data was used to estimate the number of people required to capture X percent of the pre-Flood diversity.
Even though it would require an average of 61 people to capture 99% of current diversity, the Ark passengers could have carried nearly 80% of the then-circulating alleles.
Also, pre-Flood mutations were more likely to have been lost than created alleles.
Even so, over 20% of created alleles should have been lost. This could have played a role in the approximately 90% decline in lifespan between the antediluvian Patriarchs and today, although one would not expect a continuing decline in diversity because the rapid expansion of the post-Flood population would have cancelled out most of the effects of genetic drift.
There were eight passengers on the Ark, but there were not eight founders of the post-Flood population. Not only are no additional children recorded for Noah and his wife, but Genesis 9:18–19
specifically claims that Shem, Ham, and Japheth are the ancestors of the “people of the whole earth”.
But since the three founding males were all brothers, we need to take an inbreeding coefficient into account. This would have reduced the ‘effective’ population size to less than six people.
People carry two haploid copies of the human genome. Due to chromosomal recombination, any portion of either copy has a probability of inheritance of ½ per child. Thus, the three brothers combined do not equate to six haploid genomes, because their parents only carried four haploid genomes between them. Yet, since they represented a subsampling of the four haploid genomes of their parents, portions of the genomes of Noah and his wife may have been lost.
For any given heterozygous allele, there is a 25% probability that only one of the two alleles will be passed by one of the parents to all three sons. In these cases, the alternate allele is lost forever. Thus, approximately ¼ of Noah’s allelic diversity and ¼ of his wife’s allelic diversity should have been lost.
Instead of carrying the entire genome of both Noah and his wife,
the brothers carried only 75% of each. In the end, Shem, Ham, and Japheth equate to only 1.5 people. Thus, the effective population size on the Ark was, at most, 3 + 2 – (0.53× 2), or 4.75 people.
However, if the three daughters-in-law are closely related, to each other or to the three brothers, the inbreeding coefficient will be even stronger, and the effective population size will be that much lower.
If the daughters-in-law are actual daughters (sisters to the three brothers), only the genomes of Noah and his wife could possibly have made it through the Flood. But, some small portion of their genetic diversity would still have been lost, despite the six-fold sampling. The effective population size in this case would be 2 – (0.56× 2) =1.96875.
How much of the antediluvian genetic diversity did the Flood bottleneck wipe out if there was an effective population size of only 4.75 individuals on the Ark? Would the bottleneck have produced catastrophic levels of inbreeding?
The HapMap database can be used to answer questions like these. It was designed to sample a significant fraction of the most common genetic variants carried by modern humans.
To that end, they sequenced 1.6 million single letters scattered throughout the genomes of 1,301 people from 11 diverse world populations. The sampling strategy was designed to cover approximately 10% of the total diversity found in the human genome, and there was an average of less than 2,000 nucleotides between the variants they sampled.
The HapMap Project has been mostly superseded by larger genomics programs like the completed 1,000 Genomes Project or the upcoming 100,000 Genomes (UK) and 1,000,000 Genomes (US) efforts. However, the original HapMap data are excellent for the purposes of elucidating multiple aspects of the genetics of creation.
The majority of created diversity alleles should have been on the Ark. Even though it would require dozens of people to capture 95% or more of the pre-Flood diversity, the Ark passengers would have captured at least the majority of alleles even in the worst-case scenarios. Rounding off, we can conclude that on the order of 60–80% of pre-Flood diversity should have been retained through the Flood.
In the simplest model, God created Adam’s genome with millions of heterozygous alleles.
Any variation that Adam carried would have had an initial frequency of 0.5.
Since Eve was manufactured from Adam’s flesh, a simplifying
assumption is that she would have carried any heterozygous sites he did, with the exception of Adam’s Y chromosome, while Adam’s X chromosome would have been doubled in Eve.
An alternate model has Eve being a haploid clone of Adam, meaning all alleles start out at a frequency of 0.75, 0.5, or 0.25. There are other, more complex models where, for instance, God engineered multiple different genomes into the reproductive cells of both Adam and Eve.
All people who came after Adam and Eve (with the exception of Jesus) had to have been produced by normal sexual reproduction, but there is really no limit to the amount of diversity that could have been front-loaded into Adam and Eve. In this case, the allelic diversity of the pre-Flood world would have depended on how many children they had.
The Flood, instead of having a negative effect, would have removed a good deal of the antediluvian mutation burden, to the extent that it existed. Some of the remaining mutations could have drifted to higher frequencies during the post-Flood population rebound, but the number should not have been extreme.
In the end, we can see the effects of the Flood bottleneck. It would have removed some of the pre-Flood diversity. That is impossible to ignore. However, most of the diversity, especially most of the created diversity, should have made it through the bottleneck and, thus, should still be around today."
CMI
According to Scripture, the entire world population was reduced to three reproducing couples.
The maximum effective population size of the Ark-borne population was calculated to be 4.75 individuals (carrying the equivalent of 9.5 haploid genomes).
What effect would this have had on allelic diversity today?
How much ‘created diversity’ would have been lost?
The HapMap data was used to estimate the number of people required to capture X percent of the pre-Flood diversity.
Even though it would require an average of 61 people to capture 99% of current diversity, the Ark passengers could have carried nearly 80% of the then-circulating alleles.
Also, pre-Flood mutations were more likely to have been lost than created alleles.
Even so, over 20% of created alleles should have been lost. This could have played a role in the approximately 90% decline in lifespan between the antediluvian Patriarchs and today, although one would not expect a continuing decline in diversity because the rapid expansion of the post-Flood population would have cancelled out most of the effects of genetic drift.
There were eight passengers on the Ark, but there were not eight founders of the post-Flood population. Not only are no additional children recorded for Noah and his wife, but Genesis 9:18–19
But since the three founding males were all brothers, we need to take an inbreeding coefficient into account. This would have reduced the ‘effective’ population size to less than six people.
People carry two haploid copies of the human genome. Due to chromosomal recombination, any portion of either copy has a probability of inheritance of ½ per child. Thus, the three brothers combined do not equate to six haploid genomes, because their parents only carried four haploid genomes between them. Yet, since they represented a subsampling of the four haploid genomes of their parents, portions of the genomes of Noah and his wife may have been lost.
For any given heterozygous allele, there is a 25% probability that only one of the two alleles will be passed by one of the parents to all three sons. In these cases, the alternate allele is lost forever. Thus, approximately ¼ of Noah’s allelic diversity and ¼ of his wife’s allelic diversity should have been lost.
Instead of carrying the entire genome of both Noah and his wife,
However, if the three daughters-in-law are closely related, to each other or to the three brothers, the inbreeding coefficient will be even stronger, and the effective population size will be that much lower.
If the daughters-in-law are actual daughters (sisters to the three brothers), only the genomes of Noah and his wife could possibly have made it through the Flood. But, some small portion of their genetic diversity would still have been lost, despite the six-fold sampling. The effective population size in this case would be 2 – (0.56× 2) =1.96875.
How much of the antediluvian genetic diversity did the Flood bottleneck wipe out if there was an effective population size of only 4.75 individuals on the Ark? Would the bottleneck have produced catastrophic levels of inbreeding?
The HapMap database can be used to answer questions like these. It was designed to sample a significant fraction of the most common genetic variants carried by modern humans.
To that end, they sequenced 1.6 million single letters scattered throughout the genomes of 1,301 people from 11 diverse world populations. The sampling strategy was designed to cover approximately 10% of the total diversity found in the human genome, and there was an average of less than 2,000 nucleotides between the variants they sampled.
The HapMap Project has been mostly superseded by larger genomics programs like the completed 1,000 Genomes Project or the upcoming 100,000 Genomes (UK) and 1,000,000 Genomes (US) efforts. However, the original HapMap data are excellent for the purposes of elucidating multiple aspects of the genetics of creation.The majority of created diversity alleles should have been on the Ark. Even though it would require dozens of people to capture 95% or more of the pre-Flood diversity, the Ark passengers would have captured at least the majority of alleles even in the worst-case scenarios. Rounding off, we can conclude that on the order of 60–80% of pre-Flood diversity should have been retained through the Flood.
In the simplest model, God created Adam’s genome with millions of heterozygous alleles.
Any variation that Adam carried would have had an initial frequency of 0.5.
Since Eve was manufactured from Adam’s flesh, a simplifying
An alternate model has Eve being a haploid clone of Adam, meaning all alleles start out at a frequency of 0.75, 0.5, or 0.25. There are other, more complex models where, for instance, God engineered multiple different genomes into the reproductive cells of both Adam and Eve.
All people who came after Adam and Eve (with the exception of Jesus) had to have been produced by normal sexual reproduction, but there is really no limit to the amount of diversity that could have been front-loaded into Adam and Eve. In this case, the allelic diversity of the pre-Flood world would have depended on how many children they had.
The Flood, instead of having a negative effect, would have removed a good deal of the antediluvian mutation burden, to the extent that it existed. Some of the remaining mutations could have drifted to higher frequencies during the post-Flood population rebound, but the number should not have been extreme.
In the end, we can see the effects of the Flood bottleneck. It would have removed some of the pre-Flood diversity. That is impossible to ignore. However, most of the diversity, especially most of the created diversity, should have made it through the bottleneck and, thus, should still be around today."
CMI