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BioMed Research International
Volume 2013 (2013), Article ID 621604, 14 pages
http://dx.doi.org/10.1155/2013/621604
Research Article

Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets

1Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
2Department of Biostatistics, Yale University, 135 College Street, New Haven, CT 06520, USA
3Program in Computational Biology and Bioinformatics, 300 George Street, Yale University, New Haven, CT 06520, USA

Received 1 March 2013; Accepted 3 June 2013

Academic Editor: William Piel

Copyright © 2013 Francesc López-Giráldez et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Phylogenetic research is often stymied by selection of a marker that leads to poor phylogenetic resolution despite considerable cost and effort. Profiles of phylogenetic informativeness provide a quantitative measure for prioritizing gene sampling to resolve branching order in a particular epoch. To evaluate the utility of these profiles, we analyzed phylogenomic data sets from metazoans, fungi, and mammals, thus encompassing diverse time scales and taxonomic groups. We also evaluated the utility of profiles created based on simulated data sets. We found that genes selected via their informativeness dramatically outperformed haphazard sampling of markers. Furthermore, our analyses demonstrate that the original phylogenetic informativeness method can be extended to trees with more than four taxa. Thus, although the method currently predicts phylogenetic signal without specifically accounting for the misleading effects of stochastic noise, it is robust to the effects of homoplasy. The phylogenetic informativeness rankings obtained will allow other researchers to select advantageous genes for future studies within these clades, maximizing return on effort and investment. Genes identified might also yield efficient experimental designs for phylogenetic inference for many sister clades and outgroup taxa that are closely related to the diverse groups of organisms analyzed.