pblischak
commented
1 year ago Hi Liu,
Based on your results, it looks like there may be some evidence for hybridization among the ancestral lineages of the taxa you are testing. I think that is why you are getting strong evidence for hybridization for the same taxon between different triples.
Depending on what type of data you have, I would suggest running something like SNaQ or PhyNEST, which will estimate an actual phylogenetic network that may be able to infer these ancestral dynamics better.
Dear professor,
Thanks for the convinient software ! I recently applied HyDe to detect hybridization events among 11 goups. I performed analysis for all combinations of triplets , which revealed significant signals of hybridization in 186 out of 660 combinations. However, I found some confusing phenomenon in my data. I read many papers that involved HyDe, but I have not found the answers. I hope you can help me.
question 1: both of two below triplets are significant in my results, how can I determine whether B_eca1 or B_eca3 are hybrid. P1 Hybrid P2 Zscore Pvalue Gamma B_eca3 B_eca1 B_roc 27.65214517 0 0.415418127 B_eca1 B_eca3 B_eca4 22.36050636 0 0.51466702
qeestion 2: below triplets are all significant in my results. If B_eca3 is the hybrid lineage, how can I determine which group is the parental lineages of B_eca3. P1 Hybrid P2 Zscore Pvalue Gamma B_kan B_eca3 A_eca2 20.64633255 0 0.477761985 B_eca2 B_eca3 B_eca4 13.20803585 0 0.504983026 B_eca2 B_eca3 A_eca2 13.63157792 0 0.805693859 B_eca1 B_eca3 B_eca4 22.36050636 0 0.51466702 B_eca1 B_eca3 A_eca2 21.65425722 0 0.749721073
I guess I have to combine the HyDe result with other analysis to understand the whole story. But I wondered whether and how should I determine the hybrid species based on HyDe result. Best, Liu