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Abstract:
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A labeled gene tree topology that is more probable than the labeled gene tree topology matching a species tree is called anomalous. Species trees that can generate such anomalous gene trees are said to be in the anomaly zone (AZ). Here, probabilities of unranked and ranked gene tree topologies under the multispecies coalescent are considered. A ranked tree not only depicts the topological relationship among gene lineages, as an unranked tree does, but also the sequence in which the lineages coalesce. The software PRANC, which allows computing probabilities of ranked gene trees under the coalescent model, was developed to study how the parameters of the species tree simulated under a constant rate birth-death process can affect the probability that a species tree lies in the AZ. We observed that the probabilities of unranked AZs are higher and grow much faster than that of ranked AZs as the speciation rate increases. We found that branch lengths (i.e., edge weights) in the species trees should be short to produce both types of anomalous gene trees. Our simulation showed that the most probable ranked gene tree is likely to have same unranked topology as the species tree.
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