Phylogenetic rooting using minimal ancestor deviation

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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Figure 1: Schematic illustration of rooting unrooted trees.
Figure 2: MAD rooting illustrated with a eukaryotic protein phylogeny.
Figure 3: Root inference by four rooting methods in three datasets.
Figure 4: MAD root clock-likeness and ambiguity statistics in the three datasets.

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Authors

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.

Corresponding author

Correspondence to Giddy Landan.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Figure 1; Supplementary Tables 1 and 2. (PDF 221 kb)

Supplementary Table 3

Species composition in the three datasets. (XLS 59 kb)

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Tria, F., Landan, G. & Dagan, T. Phylogenetic rooting using minimal ancestor deviation. Nat Ecol Evol 1, 0193 (2017). https://doi.org/10.1038/s41559-017-0193

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