On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo
Fig 1
Example of a phylogenetic network.
The top node represents the origin and its child node is called the root of the network. Time flows from the origin node to the leaves (here A, B, C, D) so branches are directed from the top to the leaves. Each branch x is associated to a length tx, and to a population size θx. Additionally, branches x on top of a reticulation node have an inheritance probability γx representing their probability to have contributed to any individual at the top of the branch just below.