Questions about the unit of recombination rates in map file

[fuqi2515]

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.

[armando-caballero]

Yes, the unit used in the map file should be cM/Mb. Best wishes, Armando.

[fuqi2515]

Dear Armando,

Thank you for your quick reply! I will try to set a constant value to cMMb parameter.

Best, Qi