different results between MSMC and MSMC2

[JiangYuLab]

Dear @stschiff
I ran MSMC to infer the population split history using MSMC. But the results are strange, all CCR did not reach to one. So I changed to MSMC2, but the split times are different (the same color represents the same comparsion in the two plots). The domestication of studied animals are occurred about 10,000 years ago. From admixture analysis, Many populations are mixed populations, I do not know how the admixture event affect the result and which result is more credible?

Best Wishes
Zhuqing

[stschiff]

I think I would trust the MSMC2 result. If the populations are admixed, the result is difficult to interpret, as it reflects multiple ancestries. I can’t tell in general what that means. If you want to know for your scenario, run simulations that match your admixture hypothesis and see how MSMC behaves. Stephan

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On 15 Jul 2017, at 17:34, JiangYuLab ***@***.***> wrote: Dear @stschiff <https://github.com/stschiff> I ran MSMC to infer the population split history using MSMC. But the results are strange, all CCR did not reach to one. So I changed to MSMC2, but the split times are different. The domestication of studied animals are occurred about 10,000 years ago. From admixture analysis, Many populations are mixed populations, I do not know how the admixture event affect the result and which result is more credible? <https://user-images.githubusercontent.com/28444574/28240530-1b44991c-69b6-11e7-807e-1295b3972868.png> Best Wishes Zhuqing — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#29>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAbQmkmnj-7OKbkEe9xMZzaRMky60y38ks5sONwcgaJpZM4OZC7t>.

[JiangYuLab]

Dear @stschiff
Thank you. From your published paper (Aboriginal Australia http://www.nature.com/doifinder/10.1038/nature18299), you have simulated archaic admixture into modern humans, and found that only with high proportion (above 20%) can explain the different split time. In order to get a plausible result, I just select the "pure" individuals after ADMIXTURE analyses and also with high sequencing coverage (~15X-40X). Do I need to do above work before MSMC analyses? More, if the individuals are "pure" in the ADMIXTURE analyses, will it be a admixed individual? Thanks.
Best
Zhuqing