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Releasing uncurated datasets is essential for reproducible phylogenomics

Nature Ecology & Evolution volume 4, pages 1435–1437 (2020)Cite this article

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To the Editor — Phylogenetic analysis of sequence data is a keystone of most evolutionary studies. The deluge of data from next-generation sequencing has led to the routine use of phylogenomics to resolve evolutionary relationships between lineages and for investigating diverse evolutionary questions1,2,3. We warn that the current practice of only publishing curated phylogenomic datasets risks erroneous data selection in subsequent analyses and hampers reproducibility.

The power of phylogenomics derives from the assumption that most single genes possess some true, albeit sometimes weak, vertically inherited historical signal. By combining hundreds of genes, this phylogenetic signal is amplified and can provide robust support for the correct phylogeny (assuming the use of the appropriate evolutionary model). This assumption holds true only if the datasets for individual genes include sequences representing vertical evolution (orthologues). The inclusion of data reflecting different evolutionary events such as gene duplication (paralogues), lateral gene transfers (LGTs, which lead to the existence of xenologues) or contaminations will produce conflicting signals that can lead to the inference of an incorrect species tree4. It was initially argued that as long as enough vertical data were analysed, a few erroneously included paralogues or contaminants would not impact the results. This belief has largely been refuted, with data showing that even a few loci in datasets that contain hundreds of genes can massively impact the resulting topology and statistical support5.

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Fig. 1: Case example showing the importance of including all homologues during the addition of new species to phylogenomic datasets.
Fig. 2: Schematic pipeline for a standardized assembly of a phylogenomic dataset.

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Acknowledgements

E.D.S. was supported by the International Mobilities of Researchers of the Biology Centre (grant no. CZ.02.2.69/0.0/0.0/16_027/0008357). L.E. is supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC Starting grant no. 803151). M.W.B. was supported by the United States National Science Foundation Division of Environmental Biology (grant no. 1456054). M.K. was supported by Fellowship Purkyně (Czech Academy of Sciences) and by the project Centre for research of pathogenicity and virulence of parasites r.n.: CZ.02.1.01/0.0/0.0/16_019/0000759.

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Authors and Affiliations

  1. Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic

    Eric D. Salomaki & Martin Kolisko

  2. Unité d’Ecologie, Systématique et Evolution, CNRS, Université Paris-Saclay, Orsay, France

    Laura Eme

  3. Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA

    Matthew W. Brown

  4. Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, USA

    Matthew W. Brown

  5. Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic

    Martin Kolisko

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  1. Eric D. Salomaki
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  2. Laura Eme
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Contributions

E.D.S., L.E., M.W.B. and M.K. conceived the idea. E.D.S. and M.K. drafted the initial manuscript. E.D.S., L.E., M.W.B. and M.K. edited the manuscript.

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Correspondence to Martin Kolisko.

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Salomaki, E.D., Eme, L., Brown, M.W. et al. Releasing uncurated datasets is essential for reproducible phylogenomics. Nat Ecol Evol 4, 1435–1437 (2020). https://doi.org/10.1038/s41559-020-01296-w

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