pblischak / HyDe

Hybridization detection using phylogenetic invariants
http://hybridization-detection.readthedocs.io
MIT License
41 stars 14 forks source link

Unable to understand the result #30

Closed tanwei123456 closed 1 year ago

tanwei123456 commented 1 year ago

Dear author, I've had some success using the software to run my data, but I'm a little confused about the results。

/gss1/home/gaozhh01/.local/bin/run_hyde.py -i data.txt -m map.txt -o out -n 136 -t 8 -s 689778 --prefix data.txt
 The results are as follows:

image

  Can this result be interpreted to mean that the species of zhx is a hybrid,  and  the zhx population has ∼90% of its genetic material inherited from population ying.
 I am looking forward to your reply. Thank you!
pblischak commented 1 year ago

I think there is definitely some admixture going on but it is hard to say that zhx is a hybrid, in the sense of hybrid speciation, because it shows up in other tests as a having admixed material from other species as well. Depending on the underlying tree topology, this might be a case of older hybridization. I think running something like Dsuite could be helpful to tease things apart more, or if you want to estimate an actual network, PhyloNetworks would be good to try as well

tanwei123456 commented 1 year ago

Thank you very much for your reply, which helps me a lot ?? @.***

 

------------------ 原始邮件 ------------------ 发件人: "pblischak/HyDe" @.>; 发送时间: 2023年4月13日(星期四) 上午6:19 @.>; @.**@.>; 主题: Re: [pblischak/HyDe] Unable to understand the result (Issue #30)

I think there is definitely some admixture going on but it is hard to say that zhx is a hybrid, in the sense of hybrid speciation, because it shows up in other tests as a having admixed material from other species as well. Depending on the underlying tree topology, this might be a case of older hybridization. I think running something like Dsuite could be helpful to tease things apart more, or if you want to estimate an actual network, PhyloNetworks would be good to try as well

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pblischak commented 1 year ago

You're welcome! I'm going to close the issue for now but please let me know if you have any other questions