Background: A simple and widely used approach for detecting hybridization in phylogenies is to
reconstruct gene trees from independent gene loci, and to look for gene tree incongruence.
However, this approach may be confounded by factors such as poor taxon-sampling and/or
Results: Using coalescent simulations, we investigated the potential of supernetwork methods to
differentiate between gene tree incongruence arising from taxon sampling and incomplete lineagesorting
as opposed to hybridization. For few hybridization events, a large number of independent
loci, and well-sampled taxa across these loci, we found that it was possible to distinguish incomplete
lineage-sorting from hybridization using the filtered Z-closure and Q-imputation supernetwork
methods. Moreover, we found that the choice of supernetwork method was less important than
the choice of filtering, and that count-based filtering was the most effective filtering technique.
Conclusion: Filtered supernetworks provide a tool for detecting and identifying hybridization
events in phylogenies, a tool that should become increasingly useful in light of current genome
sequencing initiatives and the ease with which large numbers of independent gene loci can be
determined using new generation sequencing technologies.
Holland, B. R., Benthin, S., Lockhart, P. J., Moulton, V., & Huber, K. T. (2008). Using supernetworks to distinguish hybridization from lineage-sorting. Bmc Evolutionary Biology, 8(202). doi: 10.1186/1471-2148-8-202
2008 Holland et al; licensee BioMed Central Ltd.
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