I’m looking for some good review articles that explain how evolutionary population genetics works. I am not looking for an argument.
In particular, I’m looking for articles that show how mutations are modeled as generating within the model. So for example, the simplistic assumption is that mutations are modeled as occurring completely randomly within a sequence. But obviously that is not strictly speaking true, since there are many types of mutations that occur at different rates. I’m looking for papers that explain models that do take this into account (if there are any). Barring that, I’m looking for papers that explain models which do not take this into account and give justifying reasons for it.
Again, I’m not looking for an argument here. My general position is that modeling mutations as occurring randomly is perfectly fine.
It’s hard to tell what you are hoping to learn but I can also recommend a postdoc in the field who is a talented teacher and a Christian. They might be willing to recommend resources to you. DM me if interested.
Don’t have any reviews for you, but in phylogenetics the most popular model of mutation (well, actually, of substitution, which is a bit different) is GTR+I+gamma. GTR means general time-reversible, in which there is a separate rate parameter for each type of point substitution A<>C, A<>G, A<>T, etc. The I part is a parameter for proportion of sites not able to vary (because of strong purifying selection), and the gamma is another parameter for the distribution of substitution rates among sites. All these can be estimated from data or assigned a priori.
One useful source is Joe Felsenstein’s book Inferring Phylogenies.
It sounds like you’re looking not so much for population genetics models per se, but more something like computer simulations of genome or chromosome evolution where different loci have variable mutation rates? I’m sure you could google for stuff like that, or just ask some chatbot to find some references.
I’m looking for models of the Darwinian mechanism. Maybe I should have said that rather than population genetics. I know the difference between substitution and mutation. I said mutations intentionally.
This is confusing. Mutation is not “the Darwinian mechanism”. Are you sure you aren’t interested in substitution, which is affected by Darwinian mechanisms?
