Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset

• DOI: 10.1016/j.cub.2023.08.026
• Publication Date: 2023-09-01T14:31:39Z
• Authors: Kasper P. Hendriks; Christiane Kiefer; Ihsan A. Al-Shehbaz; C. Donovan Bailey; Alex Hooft van Hu...; Lachezar A. Nikolov; Lars Nauheimer; Alexandre R. Zuntini; Dmitry A. German; Andreas Franzke; Marcus A. Koch; Martin A. Lysak; Óscar Toro-Núñez; Barış Özüdoğru; Vanessa R. Invernón; Nora Walden; Olivier Maurin; Nikolai M. Hay; Philip Shushkov; Terezie Mandáková; M. Eric Schranz; Mats Thulin; Michael D. Windham; Ivana Rešetnik; Stanislav Španiel; Elfy Ly; J. Chris Pires; Alex Harkess; Barbara Neuffer; Robert Vogt; Christian Bräuchler; Heimo Rainer; Steven B. Janssens; Michaela Schmull; Alan Forrest; Alessia Guggisberg; Sue Zmarzty; Brendan J. Lepschi; Neville Scarlett; Fred W. Stauffer; Ines Schönberger; Peter Heenan; William J. Baker; Félix Forest; Klaus Mummenhoff; Frederic Lens
• Keywords: Life Sciences & Biomedicine - Other Topics; Biochemistry & Molecular Biology; Biologisk systematik; 572; info:eu-repo/classification/ddc/580; Arabidopsis; Biological Systematics; mustard family; taxonomy; MULTIPLE SEQUENCE ALIGNMENT; DIPLOIDIZATION; Target capture sequencing; PLANT; Biology; Phylogeny; Taxonomy; Science & Technology; Botany; Phylogenomics; PENALIZED LIKELIHOOD; phylogenomics; Botanik; Cell Biology; Biodiversity; 15. Life on land; ARABIDOPSIS; target capture sequencing; MOLECULAR SYSTEMATICS; EVOLUTION; Tree of Life; Chemistry; Brassicaceae; Mustard family; Human medicine; DIVERSIFICATION; Life Sciences & Biomedicine; TRANSITION; BIOGEOGRAPHY

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 phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To evaluate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moderate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.