The gene tree history of a sample of DNAs. The tree is a hypothetical depiction of a true history, not to be taken as an example of a tree estimated from data. Branch tips refer to different pieces of DNA that exist at the present moment. The remainder of the diagram below the tips is a description of history. The tip of the branch at the base of the tree is undefined because the true history is not known beyond this point.
Branches refer precisely to the persistence of a DNA sequence through time.
This persistence means at times the physical persistence, but also includes numerous cases of replication when it is the information in the sequence that persists. The nodes of the tree refer precisely to those cases of DNA replication when both daughter sequences that were produced are ancestors of sequences that are represented as tips of branches. Consider a DNA that undergoes replication to form two daughter DNAs, and suppose that the replication depends upon both the DNA sequence and the local environmental resources. After replication, the fates of the daughter DNAs may be linked because they coexist under common circumstances and compete for the same pool of resources. After some time, perhaps after many rounds of replication, one group of descendants will have replaced the other, or both will have been replaced by the descendants of yet another DNA that also shares those circumstances.