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Genome-scale approaches to resolving incongruence in molecular phylogenies

Nature volume 425, pages 798–804 (2003)Cite this article

Abstract

One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. Our results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. These results have important implications for resolving branches of the tree of life.

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Figure 1: Single-gene data sets generate multiple, robustly supported alternative topologies.
Figure 2: The distribution of bootstrap values for the eight prevalent branches recovered from 106 single-gene analyses highlights the pervasive conflict among single-gene analyses.
Figure 3: Extensive incongruence between trees derived from the 106 individual-gene data sets.
Figure 4: Phylogenetic analyses of the concatenated data set composed of 106 genes yield maximum support for a single tree, irrespective of method and type of character evaluated.
Figure 5: A minimum of 20 genes is required to recover >95% bootstrap values for each branch of the species tree.
Figure 6: Concatenation of genes supporting alternative branches leads to further amplification of bias.

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Acknowledgements

We are grateful to P. Cliften, M. Johnston and the Washington University Genome Sequencing Center for access to genome sequence data for S. kudriavzevii, S. castellii and S. kluyveri; the staff of the Saccharomyces Genome Database (http://www.yeastgenome.org/) for access to genome sequence data for S. cerevisiae, S. paradoxus, S. mikatae and S. bayanus; and the Stanford Genome Technology Center website (http://www-sequence.stanford.edu/group/candida) for access to sequence data for C. albicans. We thank D. Baum, B. Hersh, C. Hittinger and K. Johnson for useful comments on the manuscript, D. Baum and members of the Carroll laboratory for useful discussions on phylogenetics, and D. Lautenschleger for computer support. A.R. is a Human Frontier Science Program long-term fellow, B.L.W. and N.K. are NIH post-doctoral fellows, and S.B.C. is an investigator of the Howard Hughes Medical Institute. This work was funded by the Howard Hughes Medical Institute.

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  1. Antonis Rokas and Barry L. Williams: These authors contributed equally to this work

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  1. Howard Hughes Medical Institute, Laboratory of Molecular Biology, R. M. Bock Laboratories, University of Wisconsin-Madison, 1525 Linden Drive, Madison, Wisconsin, 53706, USA

    Antonis Rokas, Barry L. Williams, Nicole King & Sean B. Carroll

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Rokas, A., Williams, B., King, N. et al. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425, 798–804 (2003). https://doi.org/10.1038/nature02053

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