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Preprints, Working Papers, ... Year : 2022

Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

Kasper Hendriks
Christiane Kiefer
Ihsan Al-Shehbaz
  • Function : Author
C. Donovan Bailey
  • Function : Author
Alex Hooft van Huysduynen
Lachezar Nikolov
Lars Nauheimer
Alexandre Zuntini
Dmitry German
Andreas Franzke
Marcus Koch
Martin Lysak
Óscar Toro-Núñez
Barış Özüdoğru
Nora Walden
Olivier Maurin
Nikolai Hay
Philip Shushkov
Terezie Mandáková
Mats Thulin
Michael Windham
Ivana Rešetnik
Stanislav Španiel
Elfy Ly
J. Chris Pires
Alex Harkess
Barbara Neuffer
  • Function : Author
Robert Vogt
Christian Bräuchler
Heimo Rainer
Steven Janssens
Michaela Schmull
  • Function : Author
Alan Forrest
Alessia Guggisberg
Sue Zmarzty
  • Function : Author
Brendan Lepschi
Neville Scarlett
  • Function : Author
Fred Stauffer
  • Function : Author
Ines Schönberger
Peter Heenan
William Baker
Félix Forest
Klaus Mummenhoff
Frederic Lens

Abstract

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most published family phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies between datasets. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life, or BrassiToL) based on nuclear (>1,000 genes, almost all 349 genera and 53 tribes) and plastome (60 genes, 79% of the genera, all tribes) data. We found cytonuclear discordance between nuclear and plastome-derived phylogenies, which is likely a result of rampant hybridisation among closely and more distantly related species, and highlight rogue taxa. To evaluate the impact of this rampant hybridisation on the nuclear phylogeny reconstruction, we performed four different sampling routines that increasingly removed variable data and likely paralogs. Our resulting cleaned subset of 297 nuclear genes revealed high support for the tribes, while support for the main lineages remained relatively low. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene ‘icehouse origin’ of the family. Finally, we propose five new or re-established tribes, including the recognition of Arabidopsideae, a monotypic tribe to accommodate Arabidopsis . With a worldwide community of thousands of researchers working on this family, our new, densely sampled family phylogeny will be an indispensable tool to further highlight Brassicaceae as an excellent model family for studies on biodiversity and plant biology.The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most published family phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies between datasets. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life, or BrassiToL) based on nuclear (>1,000 genes, almost all 349 genera and 53 tribes) and plastome (60 genes, 79% of the genera, all tribes) data. We found cytonuclear discordance between nuclear and plastome-derived phylogenies, which is likely a result of rampant hybridisation among closely and more distantly related species, and highlight rogue taxa. To evaluate the impact of this rampant hybridisation on the nuclear phylogeny reconstruction, we performed four different sampling routines that increasingly removed variable data and likely paralogs. Our resulting cleaned subset of 297 nuclear genes revealed high support for the tribes, while support for the main lineages remained relatively low. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene ‘icehouse origin’ of the family. Finally, we propose five new or re-established tribes, including the recognition of Arabidopsideae, a monotypic tribe to accommodate Arabidopsis . With a worldwide community of thousands of researchers working on this family, our new, densely sampled family phylogeny will be an indispensable tool to further highlight Brassicaceae as an excellent model family for studies on biodiversity and plant biology.

Dates and versions

mnhn-04062473 , version 1 (07-04-2023)

Licence

Attribution - NonCommercial - NoDerivatives

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Kasper Hendriks, Christiane Kiefer, Ihsan Al-Shehbaz, C. Donovan Bailey, Alex Hooft van Huysduynen, et al.. Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance. 2023. ⟨mnhn-04062473⟩
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