Sorry, I’m still not at all clear on what you’re trying to say. How do differences in personality traits, etc., affect mutation rates?
How does acceptance or non-acceptance of gross developmental abnormalities, most of which are not genetic in origin, affect mutation rates?
And quoting this article (I love how timely this one is…):
"Northern Ireland between about 2000 and 1500 B.C.E. Although the DNA showed the skeletons were from different populations, thanks to a dramatic genetic turnover, all four people carried the gene that causes hemochromatosis, an uncommon condition that causes excess iron to build up in the blood.
Today, Ireland has the world’s highest rates of that mutation. Bradley suggests the gene may have some advantage, perhaps helping protect against bacterial diseases or boosting iron retention in environments with poor diet. Understanding why rare conditions pop up in certain places “may help researchers today to better understand this genetic burden,” he says."
@purposenation, I split off your conversation so you didn’t have to be under my “Genetics for Dummies” heading 
Hopefully this heading is more to your liking.
Thank you, although I still reserve the right to admit that I’m a genetics dummy =)
I think this may be poorly worded, and mean to say that Ireland has the highest prevalence of this mutation present in the population, rather than suggesting this mutant actually spontaneously occurrs more frequently in Irish people.
I don’t think you realise that this has nothing to do with the assumption of fairly constant mutation rates over time though.
No.
Now I see what you are trying to say.
That’s really, really bad writing and it’s not your fault that you misunderstand.
The genetically correct way to write that is, “Today, Ireland has the world’s highest frequency of that mutant allele.”
Unfortunately, this misleading shorthand is used far too often by those who don’t do genetics.
The mutation only happened once AFAWK. Mutations are events that create mutant alleles. Alleles are different versions of genes. You are asking about allele frequencies, not mutation rates.
@swamidass: this is an interesting question. Recent studies show that a good percentage of the human genome consists of “mobile elements”.
Since MEs are not associated with the traditional understanding of mutations (like spot changes), would this impact the calculation of mutations rates/the overall conclusions regarding bottle necks?
Do the assumptions inputed into your calculations account for MEs?
The mutation rate we uses takes ME into account.
No. The number of ME insertions is a tiny fraction of the number of point mutations, so even if you didn’t take them into account it wouldn’t matter.
Can you supply me with the data showing a consistent mutation rate over the last 100,000 years in various human populations? Including a Group A type population? How would we know its mutation rate if we had no way to find it or isolate it?
So you don’t agree with @swamidass that in my example, we might not be able to identify the correct bottleneck population size and timing?
@purposenation we are going to be doing this in detail with RTB. If I can get permission, would you like to participate in this workshop as an observer?
This is a little confusing. The paper i attached says 50% of the human genome are “contributed to” by MEs.
Doesn’t look like a tiny percentage.
What are the mutation rates used? It would be helpful if these were standard units of measure that could be easily explained to anyone reading the study, “The mutation rate is 2 for the most recent 10,000 years, and then 3 for the prior 10,000… or whatever.” Again forgive my ignorance on this, but seems like these could be explained in a way for laypeople to understand them and in consistent units of measure.
If the mutation rate for Group A is 2 and the mutation rate of Group B is 10 (again, making this up), what is the average human population rate assumed?
The mutation rates that are used seem to be highly dependent on recent data (say last 15,000 years) and seem to assume uniformity across all human populations, rather than considering that groups of isolated human groups, esp. extending back beyond 15,000 years could have had vary different mutation rates.
The mutation rates also seem to be a “tops down” approach vs. a bottom’s up approach, built upon models of different populations having different rates.
And again, my original question was more around what sensitivity analysis may have been done around potentially wide ranges of mutation rates used.
Could a given mutation rate give a bottleneck of 100 at 50,000 years? If so, why isn’t that in the range of something that is considered possible? If not, why not?
sure, happy to.
This is already explained in depth in the TMR4A thread. There is a nice figure with a link to a review. Did you not see it?
No. The mutation rate would be about 10 times higher than observered realistically in humans to produce a bottleneck at 50000. This would also be in direct conflict with data from ancient genomes.
You are confused. 50% of the genome doesn’t mean 50% of the mutations. It has nothing to do with mutation rate. ME insertions are long sequences, each of which is a single mutation, and they stick around for a long time once they’re in.
Where are you getting the idea that mutation rates change within species rapidly enough that one would have to vary that parameter?
From the TMR4A thread:
" How Much Faster for a TMR4A of 100 kya or 6 kya?
How much faster would we have to see mutation to find a TMR4A a much lower level? These numbers change with this improved estimate.
In the TMR4A thread, it seems you say that a couple at 100,000 years would have to have 5x mutation rate? Am I reading that right?
But now you say a population of 100 at 50,000 years would have to be 10x mutation rate?
And also, what sample size do we have for “ancient” human genomes at >15,000 years? It must be small? and if we don’t have them across many population groups, how do we know we are not missing some ancient DNA that has high mutation rates?