Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
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Issue date
2011-03-15Submitted date
2020-03-04Subject Terms
Animal phylogeneticsPhylogenetic analysis
Phylogenetics
Sequence alignment
Multiple alignment calculation
Evolutionary genetics
Sponges
Species diversity
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Show full item recordAbstract
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. Here, taking these three studies as a case in point, we discuss pitfalls that the simple addition of sequences cannot avoid, and show how the observed incongruence can be largely overcome and how improved bioinformatics methods can help reveal the full potential of phylogenomics.Citation
Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ, Manuel M, Wörheide G, et al. (2011) Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough. PLoS Biol 9(3): e1000602. https://doi.org/10.1371/journal.pbio.1000602Publisher
Public Library of Science (PLoS)Journal
PLoS BiologyType
Journal ArticleItem Description
© 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. The attached file is the published pdf.EISSN
1545-7885ae974a485f413a2113503eed53cd6c53
10.1371/journal.pbio.1000602
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