Christopher Alexander wrote "A City is Not a Tree" in 19651[1]. Software consultant and author of 97 Things Every Programmer Should Know Kevlin Henney has a talk titled "A System is Not a Tree"[2]. Microbiologists have known for a long time that bacteria exchange DNA in multiple ways, and their evolution is not at all neat.
It makes sense that the strict "tree" model is too simple for life, but something like a semi-lattice better describes the interaction of hybridization and other forms of gene transfer.
1 https://www.patternlanguage.com/archive/cityisnotatree.html