{"action":"created","issue":{"url":"https://api.github.com/repos/DReichLab/AdmixTools/issues/20","repository_url":"https://api.github.com/repos/DReichLab/AdmixTools","labels_url":"https://api.github.com/repos/DReichLab/AdmixTools/issues/20/labels{/name}","comments_url":"https://api.github.com/repos/DReichLab/AdmixTools/issues/20/comments","events_url":"https://api.github.com/repos/DReichLab/AdmixTools/issues/20/events","html_url":"https://github.com/DReichLab/AdmixTools/issues/20","id":217057034,"number":20,"title":"F3 test detect somewhat ancient gene flow","user":{"login":"biozzq","id":15704257,"avatar_url":"https://avatars3.githubusercontent.com/u/15704257?v=3","gravatar_id":"","url":"https://api.github.com/users/biozzq","html_url":"https://github.com/biozzq","followers_url":"https://api.github.com/users/biozzq/followers","following_url":"https://api.github.com/users/biozzq/following{/other_user}","gists_url":"https://api.github.com/users/biozzq/gists{/gist_id}","starred_url":"https://api.github.com/users/biozzq/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biozzq/subscriptions","organizations_url":"https://api.github.com/users/biozzq/orgs","repos_url":"https://api.github.com/users/biozzq/repos","events_url":"https://api.github.com/users/biozzq/events{/privacy}","received_events_url":"https://api.github.com/users/biozzq/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2017-03-26T14:49:37Z","updated_at":"2017-04-01T02:45:05Z","closed_at":null,"body":"Dear @bumblenick \r\n\r\nI 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.\r\n\r\n`snps: 16016002`\r\n                      `Source 1             Source 2               Target           f_3       std. err           Z    SNPs`\r\n `result:             ERR340334                  A14                  BS1      0.079671       0.005448      14.624 12914067`\r\n `result:             ERR340334                  A14            ERR340329      0.602950       0.036776      16.395 13012058`\r\n `result:             ERR340334                  A14            ERR340333      0.404647       0.025341      15.968 13052431`\r\n`result:             ERR340334                  A14            ERR340335      0.334453       0.020576      16.255 13053033`\r\n `result:             ERR340334                  A14            ERR340341      0.487972       0.026363      18.510 12994993`\r\n`result:             ERR340334                  A14            ERR340348      0.106602       0.006818      15.636 12944510`\r\n `result:             ERR340334                  A14           SRR1576679      0.084376       0.004683      18.016 12857869`\r\n \r\nBest\r\nZhuqing"},"comment":{"url":"https://api.github.com/repos/DReichLab/AdmixTools/issues/comments/290888704","html_url":"https://github.com/DReichLab/AdmixTools/issues/20#issuecomment-290888704","issue_url":"https://api.github.com/repos/DReichLab/AdmixTools/issues/20","id":290888704,"user":{"login":"biozzq","id":15704257,"avatar_url":"https://avatars3.githubusercontent.com/u/15704257?v=3","gravatar_id":"","url":"https://api.github.com/users/biozzq","html_url":"https://github.com/biozzq","followers_url":"https://api.github.com/users/biozzq/followers","following_url":"https://api.github.com/users/biozzq/following{/other_user}","gists_url":"https://api.github.com/users/biozzq/gists{/gist_id}","starred_url":"https://api.github.com/users/biozzq/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biozzq/subscriptions","organizations_url":"https://api.github.com/users/biozzq/orgs","repos_url":"https://api.github.com/users/biozzq/repos","events_url":"https://api.github.com/users/biozzq/events{/privacy}","received_events_url":"https://api.github.com/users/biozzq/received_events","type":"User","site_admin":false},"created_at":"2017-04-01T02:45:04Z","updated_at":"2017-04-01T02:45:04Z","body":"Dear @bumblenick \r\n\r\nThanks. Do you mean if the target population experienced a high degree of specific genetic drift after admixture, f3 will fail to be negative?  \r\n\r\nMore, 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\r\n1, the admixture event occurred in the most common ancestral of A and B\r\n2, their admixture event occurred after splitting A and B, but the admixture source may be difficult to distinguish A from B.\r\n\r\nBest Wishes\r\nZhuqing"}}
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