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  • Matters Arising
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Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact

Nature Ecology & Evolution volume 6, pages 1829–1831 (2022)Cite this article

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Matters Arising to this article was published on 24 October 2022

The Original Article was published on 13 July 2020

arising from: Fan et al. Nature Ecology and Evolution https://doi.org/10.1038/s41559-020-1239-x (2020)

Fan et al. challenge the finding that mitochondria represent a sister group to Alphaproteobacteria1, arguing that support for this position can be explained by unreliable site removal methods and outgroup attraction. The authors chose to reduce compositional heterogeneity by replacing AT-rich Rickettsiales and mitochondria with GC-rich alternatives and attempted to attenuate long branch attraction (LBA) effects by removing all fast-evolving lineages but one. The study suggests that mitochondria form a sister clade to Rickettsiales, within the ‘Alpha-II’ clade. Here we show that the association with Alpha-II is an artefact caused by a problematic taxon and that residual support for Rickettsiales-sister can be explained by convergent evolution of the selected mitochondria and Rickettsiales towards high %GC. We further argue that site removal methods are in fact reliable and that outgroup attraction is unlikely to explain the Alphaproteobacteria-sister tree.

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Fig. 1: The position of mitochondria and evolution of sequence compositions.

Data availability

The phylogenomic datasets and supermatrix alignments generated and analysed during the current study are available in the FigShare repository, https://doi.org/10.6084/m9.figshare.17108234.v1.

Code availability

The scripts count_tripartitions.py and parse_tripartition_counts.py were used to enumerate node support in ML and Bayesian phylogenies. An updated alignment_pruner.pl script was used to extract per-site heterogeneity scores (Δχ2 scores). All scripts are available at https://github.com/novigit/broCode/tree/master/nee_matters_arising

References

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Acknowledgements

We thank N. Lartillot for assistance in investigating the posterior predictive test reproducibility issue, J. Viklund for updating the alignment_pruner.pl script, and A. Roger and K. Williamson for helpful insights and discussions. Phylobayes-MPI computations were performed on resources provided by the PDC Center for High-Performance Computing (PDC) under Project SNIC 2020/5-473. This work was supported by grants from the European Research Council Consolidator (grant 817834), the Dutch Research Council (NWO; VICI grant VI.C.192.016) to T.J.G.E. and the Swedish Research Council (VR International PostDoc grant 2018-06727) to J.M.

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Authors and Affiliations

  1. Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden

    Joran Martijn & Lionel Guy

  2. Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada

    Joran Martijn

  3. Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden

    Joran Martijn

  4. Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, the Netherlands

    Julian Vosseberg

  5. NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Den Burg, the Netherlands

    Pierre Offre

  6. Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands

    Thijs J. G. Ettema

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  1. Joran Martijn
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  2. Julian Vosseberg
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  3. Lionel Guy
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  4. Pierre Offre
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  5. Thijs J. G. Ettema
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Contributions

J.M. provided the main constructive criticism of the Fan et al. manuscript and designed and carried out all analyses. J.V., L.G., P.O. and T.J.G.E. provided additional constructive criticism. J.M. and T.J.G.E. wrote, and all authors read and approved the manuscript.

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Correspondence to Joran Martijn or Thijs J. G. Ettema.

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Nature Ecology and Evolution thanks the anonymous reviewers for their contribution to the peer review of this work.

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Supplementary Information

Supplementary Materials and Methods, Texts 1–8, References, Figs. 1–41, Tables 1–6.

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Martijn, J., Vosseberg, J., Guy, L. et al. Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact. Nat Ecol Evol 6, 1829–1831 (2022). https://doi.org/10.1038/s41559-022-01871-3

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