Questions about the unit of recombination rates in map file
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Dear GONE team,
I followed the GONE tutorial to infer recent demographic history of a Drosophila species which has no empirical recombination rates estimates by using experimental methods. Thus, the third column in the map file is not available and leaves it as zeroes.
However, a good genetic map is essential to obtain reliable estimates of historical Ne. So I used the LDhelmet program (Chan et al., 2012) to perform recombination rate estimates. LDhelmet utilizes a reversible jump Markov Chain Monte Carlo model to estimate the population-scaled recombination rate. The unit of recombination rate estimated by LDhelmet is 1/bp. The below is a subset of the output file of LDhelmet for three consecutive intervals.
left_snp right_snp recombination_rate (1/bp)
6921 6928 1.4431e-01
6928 6941 1.4398e-01
6941 7049 7.3808e-02
In order to convert population-scaled recombination rates (1/bp) to (cM/Mb), I followed the methods previously described (Chan et al., 2012). Briefly, for each chromosome, we get a conversion ratio.
Conversion ratio = mean empirical chromosomal recombination rate / mean population-scaled recombination rate.
Suppose the mean empirical chromosomal recombination rate is 3 cM/Mb and the mean population-scaled recombination rate is 0.01/bp. The conversion ratio is 300cM*bp/Mb. Thus the above three interval recombination rate can be converted to cM/Mb.
left_snp right_snp recombination_rate (cM/Mb)
6921 6928 1.4431e-01300
6928 6941 1.4398e-01300
6941 7049 7.3808e-02*300
Because the Drosophila species I studied has no known empirical recombination rates, I can not convert the unit 1/bp to cM/Mb. So, my question is can I use the recombination rate (unit is 1/bp) inferred by LDhelmet in map file to estimate effective population size? Or the unit used in the map file must be cM/Mb?
Thank you for your time and help!
Best,
Qi
Reference
Chan AH, Jenkins PA, Song YS.. Genome-wide fine-scale recombination rate variation in Drosophila melanogaster. PLoS Genet. 2012;8(12):e1003090.
Yes, the unit used in the map file should be cM/Mb.
Best wishes,
Armando.
Dear Armando,
Thank you for your quick reply! I will try to set a constant value to cMMb parameter.
Best,
Qi