On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo
Table 2
Average posterior probability (PP) of the topology of network C obtained by running SnappNet on data simulated from network C.
Results are given as a function of the number of sites and as a function of the number of lineages sampled in hybrid species B and C (either both 1 or both 4). Only one lineage was sampled in every other species. Constant sites are included in the analysis and the rates u and v are considered as known. Posterior probabilities are computed on the basis of replicates for which the criterion ESS > 100 is fulfilled. The sampler efficiency (SE) is also indicated (true hyperparameter values for the prior on θ, i.e. θ ∼ Γ(1, 200); as a network prior , r ∼ Beta(1, 1),
; number of reticulations bounded by 2 when exploring the network space).