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Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

Fig 1

Example of rooted and semi-directed phylogenetic networks with h = 2 hybridization events and n = 7 sampled taxa.

Inheritance probabilities γ represent the proportion of genes contributed by each parental population to a given hybrid node. Left: rooted network modelling several biological processes. Taxon F is a hybrid between two non-sampled taxa Y and Z with γ2 ≈ 0.50, and the lineage ancestral to taxa C and D has received genes introgressed from a non-sampled taxon X, for which γ1 ≈ 0.10. An alternative process at this event could be the horizontal transfer of only a handful of genes, corresponding to a very small fraction γ1 ≈ 0.001. Center: semi-directed network for the biological scenario just described. Although the root location is unknown, its position is constrained by the direction of hybrid edges (directed by arrows). For example, C, G or E cannot be outgroups. Right: rooted network obtained from the semi-directed network (center) by placing the root on the hybrid edge that leads to taxon F (labeled by 1 − γ2).

Fig 1

doi: https://doi.org/10.1371/journal.pgen.1005896.g001