F3 test detect somewhat ancient gene flow about admixtools HOT 6 OPEN

On Sun, Mar 26, 2017 at 10:49 AM, biozzq ***@***.***> wrote: Dear @bumblenick <https://github.com/bumblenick> I have both wild and domesticated populations. From the analysis of inferred ancestral components (using admixture software), I found some wild individuals contained domesticate components (about 50%). So I want to use the three-population test to test whether these individuals have gene flow from the domesticated populations. But the results are all non-negative, meanwhile, I also do this at the individual level, the results are same as the population level. But from the results, I can see the f_3 values for these admixtured individuals (SRR1576679,BS1,ERR340348) are smaller than the unadmixtured individuals (ERR340329,ERR340333,ERR340335,ERR340341) when do analysis at individual level. I guess this admixture event may be ancient (about several thousands generations ago). So I want to know can I get some more information from the following results when the f_3 value is non-negative and can three-population test detect ancient gene flow? Thanks. snps: 16016002 Source 1 Source 2 Target f_3 std. err Z SNPs result: ERR340334 A14 BS1 0.079671 0.005448 14.624 12914067 result: ERR340334 A14 ERR340329 0.602950 0.036776 16.395 13012058 result: ERR340334 A14 ERR340333 0.404647 0.025341 15.968 13052431 result: ERR340334 A14 ERR340335 0.334453 0.020576 16.255 13053033 result: ERR340334 A14 ERR340341 0.487972 0.026363 18.510 12994993 result: ERR340334 A14 ERR340348 0.106602 0.006818 15.636 12944510 result: ERR340334 A14 SRR1576679 0.084376 0.004683 18.016 12857869 Best Zhuqing — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#20>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQn_h8xSm0yYlPQmoxKhzuWjd0UUMBPZks5rpnsBgaJpZM4Mpcxp> .

On Mon, Mar 27, 2017 at 12:26 PM, biozzq ***@***.***> wrote: Dear @bumblenick <https://github.com/bumblenick> I found I can use F4 ratio test to estimate the admixture proportions and the result seems appropriate. So I want to know whether it is normal that three-population test failed but succeeded in F4-ratio estimation. More, I do not have an accurate genetic map which just set from physical distance, does genetic map effect the results, like f3-test, D-statistic and F4-ratio test? Many thanks Best Zhuqing — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#20 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQn_h8rHUzEhUwCGaNN-Jj-PY6yJuAjvks5rp-NTgaJpZM4Mpcxp> .

On Fri, Mar 31, 2017 at 10:45 PM, biozzq ***@***.***> wrote: Dear @bumblenick <https://github.com/bumblenick> Thanks. Do you mean if the target population experienced a high degree of specific genetic drift after admixture, f3 will fail to be negative? More, when I do f4, I do not know how to chose a right combination between A and B. Should I assure the population A have no genetic contribute to B? If A have admixture with B, does it mean there are many possible for the admixture event 1, the admixture event occurred in the most common ancestral of A and B 2, their admixture event occurred after splitting A and B, but the admixture source may be difficult to distinguish A from B. Best Wishes Zhuqing — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#20 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQn_h8or2zfxfSW2uqK9Ka4mxdM_TRgLks5rrboxgaJpZM4Mpcxp> .