A phylogenetic tree describes ancestral relationships. In a probabilistic graphical model on a rooted tree, latent variables at ancestral vertices are inferred from observations at leaves using belief propagation.
It is important to note that due to horizontal gene transfer, the early days of life, and still bacteria to this day due to bacterial conjugation, are actually a graph and not a tree, see also: Figure "Graph of life".
Definitely have a look at: coral of life representations.
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