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 J. 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

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 While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve.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)
Pages (from-to)614-622
Number of pages9
JournalAmerican journal of botany
Volume105
Issue number3
DOIs
StatePublished - Mar 2018

Fingerprint

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

Keywords

  • GenBank
  • angiosperms
  • bryophytes
  • cyberinfrastructure
  • 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. (2018). A roadmap for global synthesis of the plant tree of life. American journal of botany, 105(3), 614-622. 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 J.; 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, Vol. 105, No. 3, 03.2018, p. 614-622.

Research output: Contribution to journalArticle

Eiserhardt, WL, Antonelli, A, Bennett, DJ, Botigué, LR, Burleigh, JG, Dodsworth, S, Enquist, BJ, 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, vol. 105, no. 3, pp. 614-622. 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 Mar;105(3):614-622. 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 J. ; 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 ; Vol. 105, No. 3. pp. 614-622.
@article{663129b9d1b0406980af4d50a51f6a9b,
title = "A roadmap for global synthesis of the plant tree of life",
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.",
keywords = "GenBank, angiosperms, bryophytes, cyberinfrastructure, land plant phylogeny, megaphylogenies, phylogenomics, phyloinformatics, pteridophytes, sampling",
author = "Eiserhardt, {Wolf L.} and Alexandre Antonelli and Bennett, {Dominic J.} and Botigu{\'e}, {Laura R.} and Burleigh, {J. Gordon} and Steven Dodsworth and Enquist, {Brian J.} and F{\'e}lix Forest and Kim, {Jan T.} and Kozlov, {Alexey M.} and Leitch, {Ilia J.} and Maitner, {Brian S.} and Siavash Mirarab and Piel, {William H.} and P{\'e}rez-Escobar, {Oscar A.} and Lisa Pokorny and Carsten Rahbek and Brody Sandel and Smith, {Stephen A.} and Alexandros Stamatakis and Vos, {Rutger A.} and Tandy Warnow and Baker, {William J.}",
year = "2018",
month = "3",
doi = "10.1002/ajb2.1041",
language = "English (US)",
volume = "105",
pages = "614--622",
journal = "American Journal of Botany",
issn = "0002-9122",
publisher = "John Wiley & Sons Inc.",
number = "3",

}

TY - JOUR

T1 - A roadmap for global synthesis of the plant tree of life

AU - Eiserhardt, Wolf L.

AU - Antonelli, Alexandre

AU - Bennett, Dominic J.

AU - Botigué, Laura R.

AU - Burleigh, J. Gordon

AU - Dodsworth, Steven

AU - Enquist, Brian J.

AU - Forest, Félix

AU - Kim, Jan T.

AU - Kozlov, Alexey M.

AU - Leitch, Ilia J.

AU - Maitner, Brian S.

AU - Mirarab, Siavash

AU - Piel, William H.

AU - Pérez-Escobar, Oscar A.

AU - Pokorny, Lisa

AU - Rahbek, Carsten

AU - Sandel, Brody

AU - Smith, Stephen A.

AU - Stamatakis, Alexandros

AU - Vos, Rutger A.

AU - Warnow, Tandy

AU - Baker, William J.

PY - 2018/3

Y1 - 2018/3

N2 - 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.

AB - 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.

KW - GenBank

KW - angiosperms

KW - bryophytes

KW - cyberinfrastructure

KW - land plant phylogeny

KW - megaphylogenies

KW - phylogenomics

KW - phyloinformatics

KW - pteridophytes

KW - sampling

UR - http://www.scopus.com/inward/record.url?scp=85044749049&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85044749049&partnerID=8YFLogxK

U2 - 10.1002/ajb2.1041

DO - 10.1002/ajb2.1041

M3 - Article

C2 - 29603138

AN - SCOPUS:85044749049

VL - 105

SP - 614

EP - 622

JO - American Journal of Botany

JF - American Journal of Botany

SN - 0002-9122

IS - 3

ER -