{"action":"opened","issue":{"url":"https://api.github.com/repos/stschiff/msmc/issues/42","repository_url":"https://api.github.com/repos/stschiff/msmc","labels_url":"https://api.github.com/repos/stschiff/msmc/issues/42/labels{/name}","comments_url":"https://api.github.com/repos/stschiff/msmc/issues/42/comments","events_url":"https://api.github.com/repos/stschiff/msmc/issues/42/events","html_url":"https://github.com/stschiff/msmc/issues/42","id":364955142,"node_id":"MDU6SXNzdWUzNjQ5NTUxNDI=","number":42,"title":"Effect of introgression and selfing for estimation of population split","user":{"login":"oushujun","id":5996084,"node_id":"MDQ6VXNlcjU5OTYwODQ=","avatar_url":"https://avatars2.githubusercontent.com/u/5996084?v=4","gravatar_id":"","url":"https://api.github.com/users/oushujun","html_url":"https://github.com/oushujun","followers_url":"https://api.github.com/users/oushujun/followers","following_url":"https://api.github.com/users/oushujun/following{/other_user}","gists_url":"https://api.github.com/users/oushujun/gists{/gist_id}","starred_url":"https://api.github.com/users/oushujun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/oushujun/subscriptions","organizations_url":"https://api.github.com/users/oushujun/orgs","repos_url":"https://api.github.com/users/oushujun/repos","events_url":"https://api.github.com/users/oushujun/events{/privacy}","received_events_url":"https://api.github.com/users/oushujun/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-09-28T16:16:30Z","updated_at":"2018-09-28T16:16:30Z","closed_at":null,"author_association":"NONE","body":"Hi Stephan,\r\n\r\nI want to estimate the population split of a selfing plant species using MSMC. Since the species has a very high inbreeding coefficient (0.8-0.9), I filtered out all heterozygous sites which are potentially the result of false mapping. So the data has a very long range of homozygosity, which mostly represent the true case of the species. I am wondering how selfing (or lack of heterozygous) may affect the estimation of historical Ne? From your paper, you mentioned that artifact long range of homozygosity may result in early coalescence. But I am not sure how selfing may tweak the MSMC model. I've also seen people (#28 and PSMC users) tried to generate artificial diploids to *make* heterozygous sites, does this necessary?\r\n\r\nThe other question is the effect of recent introgression. Your paper discussed about introgression at the time of population split (clean split or prolonged split). However, in my case, the ancestral population receives extensive gene flow from the split population in continuous and also recent times. Does MSMC have the ability to handle this scenario? In your paper, the masking of European ancestral regions in the MXL population seems helpful for the estimation of historical Ne, this is promising, but did you test how the masking may change the estimation of population split?\r\n\r\nThank you very much for your help!\r\nShujun\r\n"}}
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