A roadmap for global synthesis of the plant tree of life

Wolf L. Eiserhardt, Alexandre Antonelli, Dominic J. Bennett, Laura R. Botigué, J. Gordon Burleigh, Steven Dodsworth, Brian Enquist, Félix Forest, Jan T. Kim, Alexey M. Kozlov, Ilia J. Leitch, Brian S. Maitner, Siavash Mirarab, William H. Piel, Oscar A. Pérez-Escobar, Lisa Pokorny, Carsten Rahbek, Brody Sandel, Stephen A. Smith, Alexandros StamatakisRutger A. Vos, Tandy Warnow, William J. Baker

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Providing science and society with an integrated, up-to-date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non-experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re-run at regular intervals, storing trees and their metadata long-term. Providing the trees to a diverse global audience through user-friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis.

Original languageEnglish (US)
JournalAmerican Journal of Botany
DOIs
StateAccepted/In press - Jan 1 2018

Fingerprint

synthesis
phylogeny
phylogenetics
informatics
botanists
Informatics
metadata
Public Sector
Phylogeny
data quality
nucleotide sequences
DNA
methodology

Keywords

  • Angiosperms
  • Bryophytes
  • Cyberinfrastructure
  • GenBank
  • Land plant phylogeny
  • Megaphylogenies
  • Phylogenomics
  • Phyloinformatics
  • Pteridophytes
  • Sampling

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Plant Science

Cite this

Eiserhardt, W. L., Antonelli, A., Bennett, D. J., Botigué, L. R., Burleigh, J. G., Dodsworth, S., ... Baker, W. J. (Accepted/In press). A roadmap for global synthesis of the plant tree of life. American Journal of Botany. https://doi.org/10.1002/ajb2.1041

A roadmap for global synthesis of the plant tree of life. / Eiserhardt, Wolf L.; Antonelli, Alexandre; Bennett, Dominic J.; Botigué, Laura R.; Burleigh, J. Gordon; Dodsworth, Steven; Enquist, Brian; Forest, Félix; Kim, Jan T.; Kozlov, Alexey M.; Leitch, Ilia J.; Maitner, Brian S.; Mirarab, Siavash; Piel, William H.; Pérez-Escobar, Oscar A.; Pokorny, Lisa; Rahbek, Carsten; Sandel, Brody; Smith, Stephen A.; Stamatakis, Alexandros; Vos, Rutger A.; Warnow, Tandy; Baker, William J.

In: American Journal of Botany, 01.01.2018.

Research output: Contribution to journalArticle

Eiserhardt, WL, Antonelli, A, Bennett, DJ, Botigué, LR, Burleigh, JG, Dodsworth, S, Enquist, B, Forest, F, Kim, JT, Kozlov, AM, Leitch, IJ, Maitner, BS, Mirarab, S, Piel, WH, Pérez-Escobar, OA, Pokorny, L, Rahbek, C, Sandel, B, Smith, SA, Stamatakis, A, Vos, RA, Warnow, T & Baker, WJ 2018, 'A roadmap for global synthesis of the plant tree of life', American Journal of Botany. https://doi.org/10.1002/ajb2.1041
Eiserhardt WL, Antonelli A, Bennett DJ, Botigué LR, Burleigh JG, Dodsworth S et al. A roadmap for global synthesis of the plant tree of life. American Journal of Botany. 2018 Jan 1. https://doi.org/10.1002/ajb2.1041
Eiserhardt, Wolf L. ; Antonelli, Alexandre ; Bennett, Dominic J. ; Botigué, Laura R. ; Burleigh, J. Gordon ; Dodsworth, Steven ; Enquist, Brian ; Forest, Félix ; Kim, Jan T. ; Kozlov, Alexey M. ; Leitch, Ilia J. ; Maitner, Brian S. ; Mirarab, Siavash ; Piel, William H. ; Pérez-Escobar, Oscar A. ; Pokorny, Lisa ; Rahbek, Carsten ; Sandel, Brody ; Smith, Stephen A. ; Stamatakis, Alexandros ; Vos, Rutger A. ; Warnow, Tandy ; Baker, William J. / A roadmap for global synthesis of the plant tree of life. In: American Journal of Botany. 2018.
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