Questions about foreground selection in relax and absrel

[SWei2333]

Dear professor,
I am currently using HyPhy to perform analyses of positive selection and relaxed selection. However, I am encountering some issues when defining the foreground branches. My species tree is somewhat unique, with the target species divided into two main clades, where the evolutionary distances within each clade are very short. Here is one of the gene trees for reference：

unroot gene tree:
(F1{FG}:0.00070401899242838681,((F2{FG}:0.00000100000050002909,F3{FG}:0.00000100000050002909):0.00093317167330555107,(((Pob:0.17517505422499526913,(ra:0.02542929898828147697,mm:0.01695436807345358440):0.02161479586100052350):0.00863873160671891141,(Mau:0.03752917394300801096,(Aam:0.01057911674826495473,Mgl:0.02396030985925277565):0.02871436292647952526):0.00178655219347533911):0.04713392449506282472,(hg:0.05792762350589615583,(Cgundi:0.10957499030494885495,((F5{FG}:0.00069729288346535856,(F6{FG}:0.00070133847153057340,(F7{FG}:0.00070134346393212470,(F8{FG}:0.00000100000050002909,F9{FG}:0.00070203037593448295):0.00070080480656137148):0.00000100000050002909):0.00070769965971332921):0.02731837757137357825,F10{FG}:0.01962642696359662153):0.02723847499250064280):0.02343330415341404738):0.02844651408885923161):0.05679630520456295517):0.00190656402120635278,F4{FG}:0.00000100000050002909):0.0;

Given this situation, should I set the ancestral nodes of these closely related target species as the foreground branches, rather than only setting the leaf nodes as foreground branches, in order to obtain more accurate selection results?

Thank you for your help!

Best wishes

[spond]

Dear @SWei2333,

My understanding is that you are talking about "orange" branches here?

Depending on your question, you could include them. It will definitely boost the power to detect differences from the rest of the tree. The main challenge is do determine a priori, whether or not you expect the selective regimes to be different between the "orange" and the "blue" branches. If not, then feel free to combine them.

Best,
Sergei

[SWei2333]

Thank you very much for your response. Regarding whether the orange branches and blue branches are under the same selective pressure, if I were to base my judgment solely on testing, I would consider the blue species, which are closely related, have a short divergence time of about 1 million years, and share the same traits, to be under the same selective pressure. Should I perform any specific analyses to validate this assumption? Do you have any suggestions for how to approach this? Best wishes Sergei Pond ***@***.***> 于2024年11月22日周五 02:29写道：

…

Dear @SWei2333 <https://github.com/SWei2333>, My understanding is that you are talking about "orange" branches here? image.png (view on web) <https://github.com/user-attachments/assets/c448fcd7-2d5e-4c16-b8f3-ced776ac9e56> Depending on your question, you could include them. It will definitely boost the power to detect differences from the rest of the tree. The main challenge is do determine *a priori*, whether or not you expect the selective regimes to be different between the "orange" and the "blue" branches. If not, then feel free to combine them. Best, Sergei — Reply to this email directly, view it on GitHub <#1762 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BIAZCE36TUYNZRLMAAR7KIL2BYQ77AVCNFSM6AAAAABSHGWOLCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIOJRHE3TINZRGQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>