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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
Martijn, J., Vosseberg, J., Guy, L., Offre, P. & Ettema, T. J. G. Deep mitochondrial origin outside the sampled alphaproteobacteria. Nature 557, 101–105 (2018).
Fan, L. et al. Phylogenetic analyses with systematic taxon sampling show that mitochondria branch within Alphaproteobacteria. Nat. Ecol. Evol. https://doi.org/10.1038/s41559-020-1239-x (2020).
Toft, C. & Andersson, S. G. E. Evolutionary microbial genomics: insights into bacterial host adaptation. Nat. Rev. Genet. 11, 465–475 (2010).
McCutcheon, J. P. & Moran, N. A. Extreme genome reduction in symbiotic bacteria. Nat. Rev. Microbiol. 10, 13–26 (2012).
Darby, A. C., Cho, N.-H., Fuxelius, H.-H., Westberg, J. & Andersson, S. G. E. Intracellular pathogens go extreme: genome evolution in the Rickettsiales. Trends Genet. 23, 511–520 (2007).
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).
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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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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Nature Ecology and Evolution thanks the anonymous reviewers for their contribution to the peer review of this work.
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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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DOI: https://doi.org/10.1038/s41559-022-01871-3
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