Fig 2. The seven moves that the MCMC sampler utilizes can be classified into ones that do not modify the topology of the phylogenetic network (moves 1 and 2), ones that modify the topology but do not change the model’s dimensions (moves 3, 4, and 5), and ones that modify the topology and model’s dimensions (moves 6 and 7).

The current-state phylogenetic network is shown at the center in dark blue, and the resulting next-state phylogenetic network after each moves is show in black lines. Moves 1 and 2 modify branch lengths and inheritance probabilities, respectively. Moves 3–5 relocate one of the children of a tree node, relocate the head of a reticulation edge, and reverse the direction of a reticulation edge, respectively. Moves 6 and 7 add and remove a reticulation edge, respectively. The probabilities κ and ω determine which of the three groups of moves is selected in an iteration. Within each group, an edge is selected and a move is selected uniformly at random among all the ones that are applicable to the selected edge within that group.