Phylogenetic analyses with systematic taxon sampling show that mitochondria branch within Alphaproteobacteria


Though it is well accepted that mitochondria originated from an alphaproteobacteria-like ancestor, the phylogenetic relationship of the mitochondrial endosymbiont to extant Alphaproteobacteria is yet unresolved. The focus of much debate is whether the affinity between mitochondria and fast-evolving alphaproteobacterial lineages reflects true homology or artefacts. Approaches such as site exclusion have been claimed to mitigate compositional heterogeneity between taxa, but this comes at the cost of information loss, and the reliability of such methods is so far unproven. Here we demonstrate that site-exclusion methods produce erratic phylogenetic estimates of mitochondrial origin. Thus, previous phylogenetic hypotheses on the origin of mitochondria based on pretreated datasets should be re-evaluated. We applied alternative strategies to reduce phylogenetic noise by systematic taxon sampling while keeping site substitution information intact. Cross-validation based on a series of trees placed mitochondria robustly within Alphaproteobacteria, sharing an ancient common ancestor with Rickettsiales and currently unclassified marine lineages.

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Fig. 1: Relationships between alignment sites, the phylogenetic position of mitochondria and model fit (mean square heterogeneity across taxa test) based on different datasets, site-exclusion approaches and taxon-selection approaches.
Fig. 2: Schematic phylogenetic relationships of alphaproteobacterial subgroups.
Fig. 3: Schematic phylogenetic relationships of mitochondria and alphaproteobacterial subgroups.
Fig. 4: Phylogenetic relationships of mitochondria and Alpha IIb Alphaproteobacteria.

Data availability

The alignments and tree files generated in this study have been deposited in figshare ( (ref. 30).

Code availability

The script of the Bowker’s test score-based site-exclusion method is available as Supplementary Software.


  1. 1.

    Ku, C. et al. Endosymbiotic origin and differential loss of eukaryotic genes. Nature 524, 427–432 (2015).

    CAS  Article  Google Scholar 

  2. 2.

    Thiergart, T., Landan, G., Schenk, M., Dagan, T. & Martin, W. F. An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. Genome Biol. Evol. 4, 466–485 (2012).

    CAS  Article  Google Scholar 

  3. 3.

    Abhishek, A., Bavishi, A., Bavishi, A. & Choudhary, M. Bacterial genome chimaerism and the origin of mitochondria. Can. J. Microbiol. 57, 49–61 (2011).

    CAS  Article  Google Scholar 

  4. 4.

    Atteia, A. et al. A proteomic survey of Chlamydomonas reinhardtii mitochondria sheds new light on the metabolic plasticity of the organelle and on the nature of the alpha-proteobacterial mitochondrial ancestor. Mol. Biol. Evol. 26, 1533–1548 (2009).

    CAS  Article  Google Scholar 

  5. 5.

    Roger, A. J., Muñoz-Gómez, S. A. & Kamikawa, R. The origin and diversification of mitochondria. Curr. Biol. 27, R1177–R1192 (2017).

    CAS  Article  Google Scholar 

  6. 6.

    Derelle, R. & Lang, B. F. Rooting the eukaryotic tree with mitochondrial and bacterial proteins. Mol. Biol. Evol. 29, 1277–1289 (2012).

    CAS  Article  Google Scholar 

  7. 7.

    Wang, Z. & Wu, M. An integrated phylogenomic approach toward pinpointing the origin of mitochondria. Sci. Rep. 5, 7949 (2015).

    CAS  Article  Google Scholar 

  8. 8.

    Viklund, J., Ettema, T. J. & Andersson, S. G. Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade. Mol. Biol. Evol. 29, 599–615 (2012).

    CAS  Article  Google Scholar 

  9. 9.

    Esser, C. et al. A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol. Biol. Evol. 21, 1643–1660 (2004).

    CAS  Article  Google Scholar 

  10. 10.

    Fitzpatrick, D. A., Creevey, C. J. & McInerney, J. O. Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales. Mol. Biol. Evol. 23, 74–85 (2006).

    CAS  Article  Google Scholar 

  11. 11.

    Rodríguez-Ezpeleta, N. & Embley, T. M. The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria. PLoS ONE 7, e30520 (2012).

    Article  Google Scholar 

  12. 12.

    Viale, A. M. & Arakaki, A. K. The chaperone connection to the origins of the eukaryotic organelles. FEBS Lett. 341, 146–151 (1994).

    CAS  Article  Google Scholar 

  13. 13.

    Castelli, M. et al. Deianiraea, an extracellular bacterium associated with the ciliate Paramecium, suggests an alternative scenario for the evolution of Rickettsiales. ISME J. 13, 2280–2294 (2019).

    Article  Google Scholar 

  14. 14.

    Brindefalk, B., Ettema, T. J., Viklund, J., Thollesson, M. & Andersson, S. G. A phylometagenomic exploration of oceanic alphaproteobacteria reveals mitochondrial relatives unrelated to the SAR11 clade. PLoS ONE 6, e24457 (2011).

    CAS  Article  Google Scholar 

  15. 15.

    Thrash, J. C. et al. Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. Sci. Rep. 1, 13 (2011).

    Article  Google Scholar 

  16. 16.

    Georgiades, K., Madoui, M. A., Le, P., Robert, C. & Raoult, D. Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion. PLoS ONE 6, e24857 (2011).

    CAS  Article  Google Scholar 

  17. 17.

    Martijn, J., Vosseberg, J., Guy, L., Offre, P. & Ettema, T. J. G. Deep mitochondrial origin outside the sampled alphaproteobacteria. Nature 557, 101–105 (2018).

    CAS  Article  Google Scholar 

  18. 18.

    Gray, M. W., Burger, G. & Lang, B. F. Mitochondrial evolution. Science 283, 1476–1481 (1999).

    CAS  Article  Google Scholar 

  19. 19.

    Gawryluk, R. M. R. Evolutionary biology: A new home for the powerhouse? Curr. Biol. 28, R798–R800 (2018).

    CAS  Article  Google Scholar 

  20. 20.

    Blanquart, S. & Lartillot, N. A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution. Mol. Biol. Evol. 23, 2058–2071 (2006).

    CAS  Article  Google Scholar 

  21. 21.

    Muñoz-Gómez, S. A. et al. An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins. eLife 8, e42535 (2019).

  22. 22.

    Nguyen, L. T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).

    CAS  Article  Google Scholar 

  23. 23.

    Jermiin, L. S., Jayaswal, V., Ababneh, F. M. & Robinson, J. Identifying optimal models of evolution. Methods Mol. Biol. 1525, 379–420 (2017).

    CAS  Article  Google Scholar 

  24. 24.

    Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).

    Article  Google Scholar 

  25. 25.

    Lartillot, N., Rodrigue, N., Stubbs, D. & Richer, J. PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 62, 611–615 (2013).

    CAS  Article  Google Scholar 

  26. 26.

    Kannan, S., Rogozin, I. B. & Koonin, E. V. MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes. BMC Evol. Biol. 14, 237 (2014).

    Article  Google Scholar 

  27. 27.

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

    CAS  Article  Google Scholar 

  28. 28.

    Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).

    CAS  Article  Google Scholar 

  29. 29.

    Criscuolo, A. & Gribaldo, S. BMGE (block mapping and gathering with entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol. 10, 210 (2010).

    Article  Google Scholar 

  30. 30.

    Fan, L. et al. Mitochondria and Alphaproteobacteria phylogenetic study alignments and tree files. figshare (2020).

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This work was financially supported by the National Natural Science Foundation of China (91851210, 91951120, 41530105 and 81774152), the European Research Council (ERC 666053), the Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology (ZDSYS201802081843490), the Shenzhen Science and Technology Innovation Commission (JCYJ20180305123458107), the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (K19313901) and the VW foundation (93 046). Computation in this study was supported by the Centre for Computational Science and Engineering at the Southern University of Science and Technology.

Author information




L.F., W.F.M. and R.Z. conceived this study. L.F., D.W., V.G., J.X., Y.X. and S.G. were involved in data analysis. L.F., V.G., C.Z., W.F.M. and R.Z. interpreted the results and drafted the manuscript. All authors participated in the critical revision of the manuscript.

Corresponding authors

Correspondence to Lu Fan or William F. Martin or Ruixin Zhu.

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Supplementary information

Supplementary Information

Supplementary methods, references, Notes 1–9 and Figs. 1–60.

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Supplementary Table

Supplementary Tables 1–7.

Supplementary Software

The script of the Bowker’s test score-based site-exclusion method.

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Fan, L., Wu, D., Goremykin, V. et al. Phylogenetic analyses with systematic taxon sampling show that mitochondria branch within Alphaproteobacteria. Nat Ecol Evol (2020).

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