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wangke16 / MSMC-IM

A tool for estimating time-dependent migration rates based on cross-/within-population coalescent rates from MSMC
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estimating divergence time in the presence of archaic introgression #10

Open JohnsonStev opened 1 year ago

JohnsonStev commented 1 year ago

Dear Wang,

I am using MSMC-IM to investigate the demographic history of two species/populations.

The resulting m(t) graph has two peaks. The older and more prominent one I am sure comes from introgression with an outgroup species.

My question is that if I want to estimate divergence time with 50% M(t), should I do the calculation without the admixture peak or not?

Thank you.

wangke16 commented 1 year ago

Hi, good question. for calculating 50% M(t), we would suggest do the calculation with the admixture peak included, , though in such way taking 50% M(t) as the estimated divergence time could lead to underestimation on the real divergence time.