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Thanks for your response and sharing your thoughts! I wonder if there will be an intermediary period where several models are used and whichever is most appropriate is picked a la species.
I too think my professors talked about something similar, loki asgard archae things. I found a paper on developments and possible effects on the tree of life. I saw some news a while back about some meaningful progress about asgardarchaeota which I haven't looked into but might be one of the seminal works that ends up changing how we define the tree of life.
What you mentioned is true, the cross-species genetic transfer stuff is super interesting and hard for me to wrap my head around. Makes me think scRNA sequencing might be preferable since there's at least the concentration of the molecule and a time series analysis that can be done which is more straightforward.