No, there were not. Here’s what I said again… I made up the numbers as I didn’t know what good mutation rates would be.
"Let’s say there is a population of 100 people. 20 of them have a mutation rate of 10 (making this up), 20 have a rate of 11, 20 have a rate of 12, 20 have a rate of 13, 20 have a rate of 14.
If they all were equally likely to mate and produce equal numbers of offspring with equal survival rates, their effective mutation rate for this group of 100 would be 12 (I think?).
However, if only those with a rate of 14 were allowed to reproduce, the effective rate for the group would actually be 14. Another group might only allow those with a 10 rate to reproduce. So the delta in effective mutation rates for the two groups, even in one generation, would be 14 vs. 10. (I think?)
Or the group of 20 people with 10’s split off from the group of 20 people of 14’s… and similar splits continued through time. We would have very heterogeneous groupings of isolated mutation rates. It’s would not be until all these groups recombine to give us the overall homogeneous and seemingly unchanging effective mutation rates we see in the last 10k-15k years."
But again, doesn’t seem to be much point in continuing this with you as I realize you find no value in it.
And, however, I’ll add that you are correct in that I should be looking at mutation rates AND allele frequencies in trying to understand the potential issues with assumptions used in bottleneck studies. But I heard from several mutation rates are the main assumption underlying these bottleneck studies, so my larger question/concern was relying to heavily on mutation rates in these studies. That’s what started the thread. And when @swamidass agreed that “Group A” in my original scenario (the first post in this thread) might not be detected, I asked more questions surrounding that.
Yes, I realized I mis-read the headline in this article:
I missed the word “lower” and thought it said “one third” but it’s “one third lower.” big difference I realize, my mistake, I’m going to correct it, sorry.
The population models don’t look at differences in phenotype. They are looking at differences in the DNA sequences themselves independent of phenotype. For this work, the mutation rate is important, not the effect a single mutation will have. We are looking at genetic diversity, not morphological diversity.
As to your questions about transposons and substitution mutations, according to the chimp genome paper there were more substition mutations than transposon insertions since the lineages split. There are 35 million substitution mutations that separate chimps and humans compared to ~13,000 transposon insertions (adding up Alu and LINE-1 insertions from Table 2 from the chimp genome paper).
The larger problem is that the average mutation rate would need to be about 10x higher than what we have evidence for in order for a relatively recent genetic A&E to work. The observed mutation rate in modern populations is in line with other evidence, such as the divergence between historic human populations and ancient human DNA. We would need to seem some evidence of much higher mutation rates before we could lean in that direction.
Linkage disequilibrium is also an issue. This deals with how genes have been shuffled around due to recombination. Pop gen isn’t my cup of tea, so I would be interested if someone else could perhaps talk on that subject.
Yes, @Ashwin_s summarized my line of questioning well. And, yes, after re-reading some of Buggs’ articles and comments, it seems he was asking similar types of questions (although he obviously is the expert, I’m still the genetics dummy).
The whole string on BioLogos from last year seemed to go into similar directions (I’m catching up on my reading, I usually don’t have time for this much reading).
But did you also accuse Buggs of being skeptical only because he was trying to defend a literal reading of the bible? Hope you will understand that I’m only being as “skeptical” as your new user name (minus the BioLogos mention) implies. =)
I guess I need to talk to Buggs next.
I’m not trying to shoot for a bottleneck of two. I’m questioning the bottleneck of 10,000 to such a high degree of certainty and asking couldn’t there have been a bottleneck of 100 within the past 50k-100k? Seems no one has answered that yet. So, if I’m willing to ask that question, and there doesn’t also seem to be a ready answer, that shows this is all about a population of two for everyone else, which is not even what I’m asking at the moment.
But I hope that also shows my intention is not to match a literal reading (or perhaps any reading) of the bible. I’m just trying to understand the population bottleneck studies and the assumptions used.
Sounds like a good challenge. But, in defending a “heliocentric certainty” type of a model, you should at least show that you have tested what kinds of bottleneck arise, lower than 10,000 in the population, when adjusting for higher ancient mutation rates over various periods of time. Why do you have to have evidence of higher mutation rates in the past, in order to test it an provide a upper/lower bound sensitivity analysis and confidence level? As I understand it, the past data we have actually does show higher mutation rates, though it seems spotty at best. @swamidass seems to have done sensitivity analysis to some degree down to a population of two. I guess my focus was not on a certainty of two, but of maybe 100 prior to 500k yo, questoining the strong claims of a population of no less than 10,000 claimed by Venema and those he cites in his book.
My understanding is that you looked at what the mutation rates would need to be to get to a population of two, but that you had indicated to me not for a population of say, 100 or 1,000. Venema claimed heliocentric certainty for 10,000.
I think we already know that Venemas claims were wildly overstated. I hope no one here is defending them. Why do you feel the need to relitigate it? We have already shown how he was wrong.
It’s not just his analysis of the studies he cites, but he’s also claiming that those studies themselves show no less than “about 10,000 population.”
Do you agree that all of the studies he cited point to a population of no less than 10,000?
I’m not just questioning his claims, but also what those studies (I have not read them, but plan to) show as a bottleneck and what kind of sensitivity analysis (for mutation and other assumptions) showed in those studies. I have a hard time believing that they did sensitivity analysis and that it required super high mutation rates (or other assumptions) to get to 1,000 or 100 bottleneck in the past 50k-100k.
I’m not sure we know precisely what the truth is, but the evidence he cites does not demonstrate it was never less than 10,000, and some of the study directly contradicts this. Veneme misunderstood these studies to be computing the minimum population size, not the average.
I’m not quesitoning them either. I’m past questioning them. I know they were wrong.
As do I. None of the work we are doing relies on Venema. There were severe overstatements of the science there. That is not the approach we took.
@swamidass seems we do have evidence for higher mutation rates in the past for humans and for modern chimps, but perhaps not “much higher.” So my commentary was that sounds like a good challenge… to find evidence of “much higher” rates, but not sure what would satisfy “much higher…” 2x?
That is an interesting question. I do not think we have the data for this with the methods I am using.
Based on other models, it is possible I think that there was a dip to a couple thousand at the Toba erruption about 70 kya. They were likely spread across the globe. Is that what you are aiming for?
Perhaps 2 at 500 kya, but this is somewhat tentative becuase it doesn’t take into account Neanderthal dievereance. I think with full data (including neanderthal), it will push back to 700 kya. I’m not sure there is any substantial difference between 700 - 400 kya for theology.
big difference I realize, my mistake, I’m going to correct it, sorry.