A roadmap for global synthesis of the plant tree of life

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

doi:10.1002/ajb2.1041

A roadmap for global synthesis of the plant tree of life

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

^*Corresponding author for this work

Department of Biology - Ecoinformatics and Biodiversity

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

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 While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve.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 language	English
Journal	American Journal of Botany
Volume	105
Issue	3
Pages (from-to)	614-622
Number of pages	9
ISSN	0002-9122
DOIs	https://doi.org/10.1002/ajb2.1041
Publication status	Published - Mar 2018

Keywords

angiosperms
bryophytes
GenBank
cyberinfrastructure
land plant phylogeny
megaphylogenies
phylogenomics
phyloinformatics
pteridophytes
sampling
LAND PLANTS
GENE TREES
SYNONYMOUS SUBSTITUTIONS
SPECIES TREES
PHYLOGENIES
INFERENCE
GENOME
DIVERSITY
INFORMATION
DATABASE

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10.1002/ajb2.1041

Cite this

Eiserhardt, W. L., Antonelli, A., Bennett, D. J., Botigue, L. R., Burleigh, J. G., Dodsworth, S., Enquist, B. J., Forest, F., Kim, J. T., Kozlov, A. M., Leitch, I. J., Maitner, B. S., Mirarab, S., Piel, W. H., Perez-Escobar, O. A., Pokorny, L., Rahbek, C., Sandel, B., Smith, S. A., ... 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

@article{6433a084a5e44c79adc80013f82c8aca,

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 = "angiosperms, bryophytes, GenBank, cyberinfrastructure, land plant phylogeny, megaphylogenies, phylogenomics, phyloinformatics, pteridophytes, sampling, LAND PLANTS, GENE TREES, SYNONYMOUS SUBSTITUTIONS, SPECIES TREES, PHYLOGENIES, INFERENCE, GENOME, DIVERSITY, INFORMATION, DATABASE",

author = "Eiserhardt, {Wolf L.} and Alexandre Antonelli and Bennett, {Dominic J.} and Botigue, {Laura R.} and Burleigh, {J. Gordon} and Steven Dodsworth and Enquist, {Brian J.} and Felix 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 Perez-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 = mar,

doi = "10.1002/ajb2.1041",

language = "English",

volume = "105",

pages = "614--622",

journal = "American Journal of Botany",

issn = "0002-9122",

publisher = "John Wiley & Sons, Ltd",

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Eiserhardt, WL, Antonelli, A, Bennett, DJ, Botigue, LR, Burleigh, JG, Dodsworth, S, Enquist, BJ, Forest, F, Kim, JT, Kozlov, AM, Leitch, IJ, Maitner, BS, Mirarab, S, Piel, WH, Perez-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

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 - Botigue, Laura R.

AU - Burleigh, J. Gordon

AU - Dodsworth, Steven

AU - Enquist, Brian J.

AU - Forest, Felix

AU - Kim, Jan T.

AU - Kozlov, Alexey M.

AU - Leitch, Ilia J.

AU - Maitner, Brian S.

AU - Mirarab, Siavash

AU - Piel, William H.

AU - Perez-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 - angiosperms

KW - bryophytes

KW - GenBank

KW - cyberinfrastructure

KW - land plant phylogeny

KW - megaphylogenies

KW - phylogenomics

KW - phyloinformatics

KW - pteridophytes

KW - sampling

KW - LAND PLANTS

KW - GENE TREES

KW - SYNONYMOUS SUBSTITUTIONS

KW - SPECIES TREES

KW - PHYLOGENIES

KW - INFERENCE

KW - GENOME

KW - DIVERSITY

KW - INFORMATION

KW - DATABASE

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U2 - 10.1002/ajb2.1041

DO - 10.1002/ajb2.1041

M3 - Journal article

C2 - 29603138

SN - 0002-9122

VL - 105

SP - 614

EP - 622

JO - American Journal of Botany

JF - American Journal of Botany

IS - 3

ER -

A roadmap for global synthesis of the plant tree of life

Abstract

Keywords

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Plant Biology and Biodiversity

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A roadmap for global synthesis of the plant tree of life

Abstract

Keywords

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Plant Biology and Biodiversity

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