Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
Hervé Philippe1*, Henner Brinkmann1, Dennis V. Lavrov2,D. Timothy J. Littlewood3, Michael Manuel4, Gert Wörheide5,6, Denis Baurain7
1 Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montréal, Québec, Canada, 2 Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, United States of America, 3 Department of Zoology, The Natural History Museum, London, United Kingdom, 4 Université Paris 6, UMR 7138 "Systématique, Adaptation, Evolution" UPMC CNRS IRD MHNH, Paris, France, 5 Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, München, Germany, 6 GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany, 7 Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
Citation: Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ, Manuel M, et al. (2011) Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough. PLoS Biol 9(3): e1000602. doi:10.1371/journal.pbio.1000602
Academic Editor: David Penny, Massey University, New Zealand
Published: March 15, 2011
Copyright: © 2011 Philippe et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: The work was funded by NSERC (www.nserc-crsng.gc.ca), CRC (www.chairs-chaires.gc.ca), Agence Nationale de la Recherche (http://www.agence-nationale-recherche.fr/), ARC Biomod (www.cfwb.be), and DFG (http://www.dfg.de/en/index.jsp). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Abbreviations: BS, bootstrap support; EST, expressed sequence tag; LBA, long branch attraction
* E-mail: herve.philippe@umontreal.ca
In the quest to reconstruct the Tree of Life, researchers have increasingly turned to phylogenomics, the inference of phylogenetic relationships using genome-scale data (Box 1). Mesmerized by the sustained increase in sequencing throughput, many phylogeneticists entertained the hope that the incongruence frequently observed in studies using single or a few genes [1] would come to an end with the generation of large multigene datasets. Yet, as so often happens, reality has turned out to be far more complex, as three recent large-scale analyses, one published in PLoS Biology [2]–[4], make clear. The studies, which deal with the early diversification of animals, produced highly incongruent (Box 2) findings despite the use of considerable sequence data (see Figure 1). Clearly, merely adding more sequences is not enough to resolve the inconsistencies.
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