Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Phylogenetic rooting using minimal ancestor deviation

Nature Ecology & Evolution volume 1, Article number: 0193 (2017) Cite this article

Subjects

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

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.

Similar content being viewed by others

References

  1. Fitch, W. M. & Margoliash, E. Construction of phylogenetic trees. Science 155, 279–284 (1967).

    Article  CAS  PubMed  Google Scholar 

  2. Ragan, M. A. Trees and networks before and after Darwin. Biol. Direct 4, 43 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  3. Kluge, A. G. & Farris, J. S. Quantitative phyletics and the evolution of anurans. Syst. Biol. 18, 1–32 (1969).

    Article  Google Scholar 

  4. Farris, J. S. Estimating phylogenetic trees from distance matrices. Am. Nat. 106, 645–668 (1972).

    Article  Google Scholar 

  5. Lepage, T., Bryant, D., Philippe, H. & Lartillot, N. A general comparison of relaxed molecular clock models. Mol. Biol. Evol. 24, 2669–2680 (2007).

    Article  CAS  PubMed  Google Scholar 

  6. Williams, T. A. et al. New substitution models for rooting phylogenetic trees. Phil. Trans. R. Soc. B 370, 20140336 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  7. Stechmann, A. & Cavalier-Smith, T. Rooting the eukaryote tree by using a derived gene fusion. Science 297, 89–91 (2002).

    Article  CAS  PubMed  Google Scholar 

  8. 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).

    Article  PubMed  PubMed Central  Google Scholar 

  9. 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).

    Article  CAS  PubMed  Google Scholar 

  10. 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).

    Article  PubMed  PubMed Central  Google Scholar 

  11. Bapteste, E. et al. Prokaryotic evolution and the tree of life are two different things. Biol. Direct 4, 34 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  12. 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).

    Article  CAS  PubMed  Google Scholar 

  13. 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).

    Article  CAS  PubMed  Google Scholar 

  14. 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).

    Article  PubMed  Google Scholar 

  15. 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).

    Article  CAS  PubMed  Google Scholar 

  16. 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).

    Article  PubMed  Google Scholar 

  17. Markowitz, V. M. et al. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 42, D560–D567 (2014).

    Article  CAS  PubMed  Google Scholar 

  18. 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).

    Article  CAS  PubMed  Google Scholar 

  19. Tatusov, R. L., Koonin, E. V. & Lipman, D. J. A genomic perspective on protein families. Science 278, 631–637 (1997).

    Article  CAS  PubMed  Google Scholar 

  20. Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European molecular biology open software suite. Trends Genet. 16, 276–277 (2000).

    Article  CAS  PubMed  Google Scholar 

  21. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Thiergart, T., Landan, G. & Martin, W. F. Concatenated alignments and the case of the disappearing tree. BMC Evol. Biol. 14, 266 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  23. Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Author notes

  1. Fernando Domingues Kümmel Tria and Giddy Landan: These authors contributed equally to this work.

Authors and Affiliations

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

    Fernando Domingues Kümmel Tria, Giddy Landan & Tal Dagan

Authors
  1. Fernando Domingues Kümmel Tria
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Giddy Landan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tal Dagan
    View author publications

    You can also search for this author in PubMed Google Scholar

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.

Ethics declarations

Competing interests

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)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1038/s41559-017-0193

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing