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Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
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2011-03-15
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2020-03-04
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Animal phylogenetics
Phylogenetic analysis
Phylogenetics
Sequence alignment
Multiple alignment calculation
Evolutionary genetics
Sponges
Species diversity
Phylogenetic analysis
Phylogenetics
Sequence alignment
Multiple alignment calculation
Evolutionary genetics
Sponges
Species diversity
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Abstract
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.
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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.1000602
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© 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.
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1545-7885