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Open Access Methodology article

Rooted triple consensus and anomalous gene trees

Gregory B Ewing*, Ingo Ebersberger, Heiko A Schmidt and Arndt von Haeseler

Author Affiliations

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Dr. Bohr Gasse 9, A-1030 Vienna, Austria

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BMC Evolutionary Biology 2008, 8:118  doi:10.1186/1471-2148-8-118

Published: 25 April 2008

Abstract

Background

Anomalous gene trees (AGTs) are gene trees with a topology different from a species tree that are more probable to observe than congruent gene trees. In this paper we propose a rooted triple approach to finding the correct species tree in the presence of AGTs.

Results

Based on simulated data we show that our method outperforms the extended majority rule consensus strategy, while still resolving the species tree. Applying both methods to a metazoan data set of 216 genes, we tested whether AGTs substantially interfere with the reconstruction of the metazoan phylogeny.

Conclusion

Evidence of AGTs was not found in this data set, suggesting that erroneously reconstructed gene trees are the most significant challenge in the reconstruction of phylogenetic relationships among species with current data. The new method does however rule out the erroneous reconstruction of deep or poorly resolved splits in the presence of lineage sorting.