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I heard several times that two SNPs, that have at least 1'000 nucleotides between them, can be seen as 'unlinked' due to frequent recombination events. I also once saw a paper showing a graph "degree of linkage vs. genetic distance". Unfortunately I can't remember which paper it was. Does anyone know where this number (1000) comes from?

PS: I'm aware that this topic is much more complex, especially if you are interested selective sweeps.

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I think you must have misremembered what you heard.

The cut-off distance for genetic linkage is 50 centimorgans which corresponds to 50% recombination. In the human genome 1 centimorgan is approximately 106 base pairs, so the 'unlinked distance' is 5 * 107 base pairs.

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  • $\begingroup$ Do you have a citation for that? $\endgroup$ – R_User Feb 24 '14 at 16:04
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    $\begingroup$ Well, you could start at the Wikipedia page for centimorgan - that's where I got the 1,000,000 base pairs from. The table at nature.com/nature/journal/v409/n6822/fig_tab/409951a0_T1.html gives some real values, which illustrate how it varies. If "unlinked" equated to 1,000 base pairs, classic genetic mapping which relied upon measuring linkage between genes would have been impossible - everything would have been unlinked. $\endgroup$ – Alan Boyd Feb 24 '14 at 16:11
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    $\begingroup$ I totally agree with @AlanBoyd. One cannot ask whether an approximation is reasonable or not without specifying the model of interest. Depending on the model of consideration some level of recombination might be enough so that you could consider two loci to be unlinked. I have never seen this kind of approximation though! $\endgroup$ – Remi.b Feb 24 '14 at 18:53

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