Learning goal: How do we go from local signals of introgression (triplets/windows) to claims about historical hybridization between clades?

Activity 1: HyDe Triplet Mining (20 min)

Let’s look in groups at the HyDe output tables. We want to find strong signals of hybridization:

• Which triplets have hybridization index far from 0 or 1?
• Which taxa repeatedly appear as “hybrids”?
• Does the same taxon show signals with different parental pairs?
• Are there contradictions?

If all these signals were true simultaneously, what kind of evolutionary history do we need to explain?

Activity 2: From taxa to clades (20 min)

Using the information from HyDe, let’s propose evolutionary scenarios (gene flow arrows) that explain the patterns we observe. How do our hypothesis compare to the authors’ Figure 5?