Rooted triple consensus and anomalous gene trees.
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.


CONCLUSIONS
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.
Ewing
Gregory B
GB
Center for Integrative Bioinformatics Vienna, Max F, Perutz Laboratories, Dr, Bohr Gasse 9, A-1030 Vienna, Austria. gregory.ewing@univie.ac.at
Ebersberger
Ingo
I
Schmidt
Heiko A
HA
von Haeseler
Arndt
A
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D049810:Genetic Speciation; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny