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Evolutionary Genomics pp 53–79Cite as

Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 856))

Abstract

Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article, we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distance method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the application of these methods to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a “species tree.”

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Abbreviations

CMDS:

Classical multidimensional scaling

COG:

Clusters of orthologous genes

BSD:

Boot-split distance

FOL:

Forest of life

HGT:

Horizontal gene transfer

ND:

Nodal distance

NUTs:

Nearly universal trees

QT:

Quartet topology

TNT:

Tree-net trend

TOL:

Tree of life

SD:

Split distance

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Acknowledgments

The authors’ research is supported by the Department of Health and Human Services intramural program (NIH, National Library of Medicine).

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Authors and Affiliations

  1. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

    Pere Puigbò, Yuri I. Wolf & Eugene V. Koonin

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  1. Pere Puigbò
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  2. Yuri I. Wolf
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  3. Eugene V. Koonin
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Correspondence to Eugene V. Koonin .

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  1. Department of Computer Science, ETH Zürich, Universitätsstr. 6, Zürich, 8092, Switzerland

    Maria Anisimova

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Puigbò, P., Wolf, Y.I., Koonin, E.V. (2012). Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life. In: Anisimova, M. (eds) Evolutionary Genomics. Methods in Molecular Biology, vol 856. Humana Press. https://doi.org/10.1007/978-1-61779-585-5_3

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  • DOI: https://doi.org/10.1007/978-1-61779-585-5_3

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