Curious About Gene Flow Direction in Hybrid Detection Results of HyDe

[Jhe1004]

Dear Professor,

Great software!

But i am reaching out to discuss an issue I encountered concerning the detection of hybrids. In my analysis, I used four species: A, B, C, and D, with their species tree modeled as (((A,B),C),D). I aimed to test whether species B is a hybrid of species A and C. The results indicated that B is indeed a hybrid of A and C, with significant support (P = 0; γ = 0.3).

Your paper on Hyde interprets such results as species B being formed by hybridization between A and C. However, as I understand, Hyde might also detect similar significant results if there was gene flow from species B to C in the past. I am curious to know if the Hyde software can determine the direction of gene flow (whether from B to C or C to B), or how you would interpret this scenario.

Thank you for your time and I look forward to your insights.

Best regards,

He