Using Ldhat To Estimate Effective Population Size

Question

[GabrielMontenegro]

Hi everyone:

I am trying to use the LDhat package to estimate the population recombination rate of my samples (phased data based on genowide SNPs) to then estimate the effective population size (Ne). I have seen that you can do that (based on some publications) but I couldn't figure out the way to do that. I think that there was only some minimal algebra involved , but again I am not very sure...

I think it goes something like this:

rho = 4 Ne x r

Ne : Effective population size r : recombination rate

If I can get the recombination rate of my region, say for chromosome 1, then I could use that estimate to solve for Ne. Is there some way to get that rate? I've been exploring the deCODE website, where there is information on genetic map, but there is only the recombination rate for pair of SNPs and not for the region.

Any help would be appreciated.

Thanks in advance.

Answer 1

[Giovanni M Dall'Olio]

You may want to read how they did it in this paper: Prado-Martinez et al, Great ape genetic diversity and population history. In particular, see Figure 3 of the paper, and page 199 of the Supplementary Materials.

You can estimate the effective population size, and how it varied over time, using the psmc software.

[GabrielMontenegro]

Dear Giovanni. Thanks for the reply I will take a look at those references. Lets see how it goes.. Thanks again.

[GabrielMontenegro]

For what I see they estimate Ne based on the population mutation rate, and not the recombination rate. And is it posible to use the psmc software on genotype phased data? I don't have sequences.