Article

Phylogenetic rooting using minimal ancestor deviation

  • Nature Ecology & Evolution 1, Article number: 0193 (2017)
  • doi:10.1038/s41559-017-0193
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Abstract

Ancestor–descendent relations play a cardinal role in evolutionary theory. Those relations are determined by rooting phylogenetic trees. Existing rooting methods are hampered by evolutionary rate heterogeneity or the unavailability of auxiliary phylogenetic information. Here we present a rooting approach, the minimal ancestor deviation (MAD) method, which accommodates heterotachy by using all pairwise topological and metric information in unrooted trees. We demonstrate the performance of the method, in comparison to existing rooting methods, by the analysis of phylogenies from eukaryotes and prokaryotes. MAD correctly recovers the known root of eukaryotes and uncovers evidence for the origin of cyanobacteria in the ocean. MAD is more robust and consistent than existing methods, provides measures of the root inference quality and is applicable to any tree with branch lengths.

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Author information

Author notes

    • Fernando Domingues Kümmel Tria
    •  & Giddy Landan

    These authors contributed equally to this work.

Affiliations

  1. Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel 24118, Germany.

    • Fernando Domingues Kümmel Tria
    • , Giddy Landan
    •  & Tal Dagan

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Contributions

We thank D. Bryant, A. Kupczok and M. Wilkinson for critical comments on the manuscript. We acknowledge support from the European Research Council (grant no. 281375) and CAPES (Coordination for the Improvement of Higher Education Personnel–Brazil).

T.D., G.L. and F.D.K.T. conceived the study. F.D.K.T. and G.L. developed and implemented the method. F.D.K.T. performed all analyses. T.D., G.L. and F.D.K.T. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Giddy Landan.

Supplementary information

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    Supplementary Information

    Supplementary Figure 1; Supplementary Tables 1 and 2.

Excel files

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    Supplementary Table 3

    Species composition in the three datasets.