It seems a human tendency to organize things into hierarchies, I think our brains are likely optimized for it, but I think it's often an oversimplification. Taking biological evolution as an example, kids are taught about the evolutionary "tree of life", e.g. phylogenetic tree, wherein organisms are organized into a hierarchy of what is related to what. But while that worldview seems broadly accurate, it's definitely an oversimplification. Cross-species genetic transfer does occur in nature through various mechanisms, for instance in ring species or rare instances of viable hybridization (mules are the classic example of infertile hybrids, but fertile mules have rarely been observed in the modern era.)

It seems to me that a directed acyclic graph, rather than a tree, is a more accurate model in this case. (Directed because time always flows in one direction.)

A phylogenetic tree also fails to capture information about life that people might reasonable find interesting. Suppose for instance you want to study all organisms that fly. Bats, birds, insects and pterosaurs all fly[flew] but don't share common flying ancestors. The "flying organism" classification doesn't fit into that simple hierarchical tree.