Recombination rate per base per generation

Question

[Alice]

Hello biostars,

I am trying to understand what rho means and how it is calculated in coalescent simulations. We know for Hundon's 'ms' program for example, that cross-over rate parameter is measured by 4N0 * r (r is probability of cross-over per generation between the ends of the locus). Now I want to simulate a locus in ms using -r parameter and I know average recombination rate for my species. How can I calculate per base per generation crossover rate?

Average recombination rate is in cM\Mb, so if, let's say, human recombination rate is 2 cM\Mb, genome size is 3 * 10^9 , then 2 / 1 * 10 ^6 = 2 * 10^-6 recombinations per base pair. This is way higher than a number used by default in different papers (such as 2*10^-8). And if I divide it by 3 * 10^9, the number is so small that it does not make sense at all. I know my calculations are incorrect, but I just don't see another way to derive this parameter.

Answer 1

[rjwang]

Hey,

I don't know if you've already figured this out, but aside from the complexities of estimating recombination rate - the big problem in your estimate is conflating cM/Mb with crossovers/Mb. The genetic distance of 1 centimorgan represents only a 1% chance of crossover in the region. If you take 2cM/Mb to be (2 x 10^-2 crossovers) / (1 x 10^-6 bp), you get the 2 x 10^-8 crossovers/bp.

Answer 2

[Alice]

Answering myself.

TL;DR - it is hard to get this number.

Here is the paper about recombination rates and pop gen models: https://www.nature.com/articles/nrg1227