Unexpected Gamma Value in HyDe Analysis of Hybridization Between Two Species

[JcWukkkk]

Hello,

I encountered an strange result while using HyDe to study potential hybridization between Species A and Species B. In my preliminary test:

Used two individuals from Species A as P1 and Hybrid

Used one individual from Species B as P2

Surprisingly, the analysis returned Gamma = 0.98, suggesting that the "hybrid" individual from Species A derives 98% of its ancestry from Species B (P2) rather than from its conspecific (P1). This appears biologically counterintuitive - I would expect the inverse (Gamma ≈ 0.02, indicating 98% ancestry from P1 and 2% from P2).

I've triple-checked: Input files are correctly formatted; No sample mislabeling occurred.

I also provide a phylogenetic tree to show that Eu1 and Eu2 are the same species, and all commands are documented in the "work.sh".

Thank you for your insights! Attached are simplified input files if helpful.

Test.zip