Mantha: Genetics for Dummies

Nope, sorry, I flipped it around. 8 and 11 mutations/lump for recombination rate of 1e-8, 13 and 18 mutations/lump for recombination rate of 0.

Glad for this post since I’m definitely in the genetics for dummies category.

In this model and other population genetic evolution models, what assumptions are made for:
1). number of offspring per reproducing couple
2). frequency and mixing rate for those offspring with others within the population (including the parents themselves)
3). frequency and amount of mixing with outside populations

Are these metrics simply a constant average, or a hi-low bounds that stays static over time and throughout the population, or are they in themselves random variables that change over time?

Seems like the results would vary dramatically if the bounds on these variables are greatly expanded or contracted?

Sorry if this question doesn’t make sense, I can try asking in another way if needed.

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Ok, that makes more sense. I got an average of 10.5 mutations/lump for a recombination rate of 0, and 1.0 mutations/lump for a recombination rate of 1e-3.


In reading the UW book that @swamidass listed (thanks!), seems like a whole host of assumptions, some I listed (inbreeding, overlapping generations) and other new ones: gender mix, degrees of monogamy, reproductive fitness (although I guess the offspring number would account for that), etc.

Would seem any models should list the assumptions that are made on these factors and/or the methods used to test variations in these?

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Turns out you can start getting rid of most assumption one by one, or understand how being wrong would affect things. The methods we are currently using are data driven, and make extemely narrow and verifiable “assumptions”. I put that in quotes because we can justify and cross check all of them with evidence.

But what ARE the assumptions used in human population studies and/or where do you look to find them for a given model/published paper? I could not find these in the Sim you sent over.

Is there one source for these or is it scattered across a bunch of different studies that “rule out” using ranges for each assumption (I put “rule out” in quotes since I’m a natural skeptic, ha).

Based on historical evidence, seems like there could be wide variations in the factors I mentioned across cultures and time periods. Ironically, it seems the Bible helps to inform some of these assumptions? At least in the past ~10,000 years in Middle Eastern cultures.

Depends on the study. Which ones are you talking about?

The sim you sent over. Or pick any human genetics model, perhaps on of your own? Just looking to see an example of how these assumptions are disclosed (or not).

Good task for @jordan on his simulation.

This is just a toy example though. The best way is dialogue with a sympathetic expert, which is why Peaceful Science exists.

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Yep, and that’s what I thought I was doing. =)

If any sympathetic experts have examples of how assumptions for these types of factors that I mentioned are disclosed in a human population paper or model, I would be so grateful!

Or if they are just internal assumptions that somehow everyone who publishes the papers alread knows, I guess let me know that too… but that would just make me a lot more curious to dig deeper, not very satisfying. =)

Have you looked at this yet? Heliocentric Certainty Against a Bottleneck of Two?

I break it down in detail there. That would be the right place to start. Ask questions based on what you see there.

If you want to discuss a particular paper, that is much more concrete that asking generally about the assumptions of “human genetics models”. There are many such models - narrow it down.

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Thank you. Sorry, I’m really not trying to be difficult. I just don’t understand where to find these. I see a few assumptions listed, but do not see any of the ones I mentioned.

What is assumed for the average or upper/lower bounds range for the number of offspring for each couple? Does that change by sub-population and/or over time?

What assumptions are made for rates of inbreeding (or overlapping generations) and how do inbreeding rates change over time and across populations (if at all)?

What assumptions are made for the number of sex partners (for males and females) and how do those change over time and/or across populations (if at all)?

None of these assumptions made for the final TMR4A analysis.

Some of these assumptions are made for the “effective population size” estimates, which is why we discarded these studies after demonstrating the assumptions dramatically affect results. Relying upon these estimates was an error.

The main assumption made for TMR4A is the mutation rate, which we can directly verify both now and in the distant past. I suppose there also is the assumption that all humans descend from the same population.

Yes, if I’m thinking of this correctly, mutations that are close together on the same chromosome would tend to “lump”, and would be more likely to show similar trends for fixation. Recombination (essentially “swapping” between the homologous chromosomes) would lead to mixing of alleles and make the inheritance of the mutations more independent of one another. More recombination would contribute to less lumping.


19 posts were split to a new topic: Cooper: Assumptions in mutation rate

A post was merged into an existing topic: Cooper: Assumptions in mutation rate

A post was merged into an existing topic: Cooper: Assumptions in mutation rate

Many such defects are not inherited. Even those that are inherited would have zero effect on mutation rates.

Finally, keep in mind that survival isn’t the metric for evolution. It’s reproduction.

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I don’t understand. That appeared as a reply to a post by me, as a reply to something I posted a long time ago, and it quotes from something I replied to recently saying much the same thing as you said.