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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Fitch, W. M. & Margoliash, E. Construction of phylogenetic trees. Science 155, 279–284 (1967).
Ragan, M. A. Trees and networks before and after Darwin. Biol. Direct 4, 43 (2009).
Kluge, A. G. & Farris, J. S. Quantitative phyletics and the evolution of anurans. Syst. Biol. 18, 1–32 (1969).
Farris, J. S. Estimating phylogenetic trees from distance matrices. Am. Nat. 106, 645–668 (1972).
Lepage, T., Bryant, D., Philippe, H. & Lartillot, N. A general comparison of relaxed molecular clock models. Mol. Biol. Evol. 24, 2669–2680 (2007).
Williams, T. A. et al. New substitution models for rooting phylogenetic trees. Phil. Trans. R. Soc. B 370, 20140336 (2015).
Stechmann, A. & Cavalier-Smith, T. Rooting the eukaryote tree by using a derived gene fusion. Science 297, 89–91 (2002).
Katz, L. A., Grant, J. R., Parfrey, L. W. & Burleigh, J. G. Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life. Syst. Biol. 61, 653–660 (2012).
Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).
Ronquist, F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012).
Bapteste, E. et al. Prokaryotic evolution and the tree of life are two different things. Biol. Direct 4, 34 (2009).
Turner, S., Pryer, K. M., Miao, V. P. W. & Palmer, J. D. Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J. Eukaryot. Microbiol. 46, 327–338 (1999).
Shih, P. M. et al. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc. Natl Acad. Sci. USA 110, 1053–1058 (2013).
Dagan, T. et al. Genomes of stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biol. Evol. 5, 31–44 (2013).
Huerta-Cepas, J. et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44, D286–D293 (2016).
O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44, D733–D745 (2016).
Markowitz, V. M. et al. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 42, D560–D567 (2014).
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
Tatusov, R. L., Koonin, E. V. & Lipman, D. J. A genomic perspective on protein families. Science 278, 631–637 (1997).
Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European molecular biology open software suite. Trends Genet. 16, 276–277 (2000).
Enright, A. J., Van Dongen, S. & Ouzounis, C. A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30, 1575–1584 (2002).
Thiergart, T., Landan, G. & Martin, W. F. Concatenated alignments and the case of the disappearing tree. BMC Evol. Biol. 14, 266 (2014).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
The authors declare no competing financial interests.
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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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