Carter: Were Recombination Rates Higher in the Past?

@SFT released a mercifully short video clip from his interview with Dr. Rob Carter. Carter mentions that African populations have more recombination hotspots than Europeans, and that recombination rates should be slowing over time due to degeneration of PRDM9 binding sites. This is seemingly offered as a partial explanation against LD and TMR4A arguments against YEC.

It’s true that Africans (notably West Africans) have more recombination hotspots in their genomes (see paper below), but I’ve yet to see any evidence that this results in a substantial increase in the overall genome recombination rate, rather than simply spreading out the same amount of recombination more evenly over the genome, as it were.

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That is an interesting theory:

But it raises several questions.

  1. As @evograd notes, reduced hotspots doesn’t imply reduced recombination. It should be easy to test if they do by comparing recombination rates in Europeans vs Africans

  2. Why do Africans and Europeans have different rates of degradation of PRDM9 hotspots?

  3. What papers have studied #1 and #2?

  4. How much more recombination is necessary for a YEC timeline.

@glipsnort does you have any information that could help us here?

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  1. The table on page 13 of the supplementary PDF of the paper I linked above compares different pedigree rates, without much of a substantial difference:

  1. One reason for differences in population-specific hotpots is different alleles of PRDM9.
  1. Wouldn’t this be approximately 500,000/6,000=83x faster recombination rates, given your TMR4A results?
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And that quickly, it seems that the evidence is against his hypothesis. The number of hot spots does not relate with the total amount of recombination. So this isn’t evidence for higher recombination rates in the past.

I’m not entirely sure. It will take some thought…the issue is that recombination is inferred any time it will reduce the number of mutations required to explain the data. So I’m not sure that increasing recombination rates would even reduce the TMR4A given the data we have seen. This is subtle though…and might require doing some simulations to settle.

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@GutsickGibbon you might want to look at this too.

To fully settle this, it would be best to see the number of hotspots inferred for each of these populations.

The paper that shows the differences are due to different alleles of the protein, rather than “degradation” of the hotspot binding sites, is interesting too. Thanks for posting the link.

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Not really. It’s been known for a long time that some Africans have PRDM9 alleles that are rare outside Africa, with resulting differences in hotspot locations, but that has nothing to do with overall rates or the supposed higher degradation rate of hotspots. Since recombination takes place just fine – and at similar rates – in species that have completely lost a functioning PRDM9, this argument seems unlikely to be correct.

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Given that African Haplotype blocks are approximately half as long as European Haplotype blocks (citations below), it would seem that creationists require African recombination rates about 2x higher than European rates in order to suggest that these populations have been around for the same amount of time, no? In which case, even if we believe that the small differences in overall recombination rates in the table I cited earlier were real rather than the result of noise or a difference in study methodologies, they still wouldn’t account for the low LD of African populations, so it all comes down to this claim about recombination rates being dramatically different in the past.


and:
https://www.nature.com/articles/s41597-019-0227-y

Hi @evograd, I am Nigerian (West African). I would like to know any consequences of Africans having higher recombination rates.

Is it possible for you or anyone else to create a really simplified introduction to TMR4A and other related concepts. I have a quite a hard time keeping up with your responses (and others too) to creationist remarks on it. I would really appreciate.

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