[westurner]

How can it be acyclic? A phylogenetic tree is a DAG. Organisms sharing DNA? That's definitely a cyclic graph.

If there were Schema.org/Animal and/or schema:AnimalInstance classes, what do you list under a :breed property to indicate that e.g. one parent is breed X and another is breed Y?! That's definitely not a DAG; that looks like a feature clustering dendrogram.

DNA barcoding > Mismatches between conventional (morphological) and barcode based identification https://en.wikipedia.org/wiki/DNA_barcoding#Mismatches_betwe...

Taxonomy (biology) https://en.wikipedia.org/wiki/Taxonomy_(biology)

FWIU, there's at least one DNA-based organism naming system; IDK how much that helps resolve :Animal and :AnimalInstance if at all?

[sixstringtheory]

My assumption as someone not formally trained in advanced biology is that the phylogenetic tree has an implied arrow of time, and each node of the tree is a point where a mutation occurred that was sufficient to create a new and separate family/order/genus/etc afterwards, with leaf nodes representing species.

In this sense a cycle can’t occur because a branch would need to reach back in time and rejoin with an ancestral branch. It would be a different kind of grandfather paradox: who would be the ancestor and who the descendant in a cycle?

Maybe someone could help point out the flaws in this model.

[flobosg]

Your assumption is true, but only for rooted phylogenetic trees. In unrooted trees the node representing the most ancestral state is absent and thus no directionality can be determined.