Skip to main content
SpringerLink
Log in

Releasing uncurated datasets is essential for reproducible phylogenomics

  • Correspondence
  • Published:

From Nature Ecology & Evolution

View current issue Submit your manuscript

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

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.

References

  1. Leger, M. M. et al. Nat. Ecol. Evol. 1, 0092 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  2. Rotterová, J. et al. Curr. Biol. 30, 2037–2050 (2020).

    Article  PubMed  Google Scholar 

  3. Lax, G. et al. Nature 564, 410–414 (2018).

    Article  CAS  PubMed  Google Scholar 

  4. Siu-Ting, K. et al. Mol. Biol. Evol. 36, 1344–1356 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Shen, X.-X., Hittinger, C. T. & Rokas, A. Nat. Ecol. Evol. 1, 0126 (2017).

    Article  Google Scholar 

  6. Bapteste, E. et al. Proc. Natl Acad. Sci. USA 99, 1414–1419 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Burki, F. & Pawlowski, J. Mol. Biol. Evol. 23, 1922–1930 (2006).

    Article  CAS  PubMed  Google Scholar 

  8. Strassert, J. F. H., Jamy, M., Mylnikov, A. P., Tikhonenkov, D. V. & Burki, F. Mol. Biol. Evol. 36, 757–765 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Brown, M. W. et al. Genome Biol. Evol. 10, 427–433 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Torruella, G. et al. Mol. Biol. Evol. 29, 531–544 (2012).

    Article  CAS  PubMed  Google Scholar 

  11. Saunders, G. W., Jackson, C. & Salomaki, E. D. Mol. Phylogenet. Evol. 119, 151–159 (2018).

    Article  PubMed  Google Scholar 

Download references

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.

Author information

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

Authors
  1. Eric D. Salomaki
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Laura Eme
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Matthew W. Brown
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Martin Kolisko
    View author publications

    You can also search for this author in PubMed Google Scholar

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.

Corresponding author

Correspondence to Martin Kolisko.

Ethics declarations

Competing interests

The authors declare no competing interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41559-020-01296-w

  • Springer Nature Limited

This article is cited by

Search

Navigation