Fig 1.
The multispecies coalescent on trees and networks.
(A) The multispecies coalescent (MSC) links populations by a tree structure and allows for modeling gene genealogies within the branches of a species tree. The gene genealogy indicated by thick lines inside the species tree is incongruent with the species tree due to incomplete lineage sorting (ILS). (B) The multispecies network coalescent (MSNC) links populations by a network structure, thus allowing for reticulations events among populations. The gene genealogy indicated by thick lines inside the species network is involved in reticulation, e.g., hybridization. The gene genealogies in both panels have the same topologies, but have different probabilities under the MSC and MSNC models.
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.
Fig 3.
Phylogenetic history of the bread wheat.
(A–C) The three phylogenetic networks that comprise the 95% credible set, (D) and a plausible summary of the three networks that is consistent with the model of phylogenetic history of bread wheat (Fig 3 in [29]).
Fig 4.
Phylogenetic history of the six mosquito genomes.
(A) The single phylogenetic network in the 95% credible set sampled on the X chromosome data. (B) A summary of the three phylogenetic networks in the 95% credible set sampled on the autosome data. The dotted circle indicates the temporal order of the two reticulation events involving R cannot be discerned with confidence from the data.
Fig 5.
Phylogenetic history of the five mouse genomes.
A summary of the six phylogenetic networks that comprise the 95% credible set. The dashed circle indicates that the different networks in the 95% credible set resolve the order of the hybridization events involving MZ in different ways.
Table 1.
The 7 moves that the Metropolis-Hastings algorithm employs.