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

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Authors	HENDRIKS Kasper P KIEFER Christiane AL-SHEHBAZ Ihsan A BAILEY C Donovan HOOFT van Huysduynen Alex NIKOLOV Lachezar A NAUHEIMER Lars ZUNTINI Alexandre R GERMAN Dmitry A FRANZKE Andreas KOCH Marcus A LYSÁK Martin TORO-NUNEZ Oscar OZUDOGRU Baris INVERNON Vanessa R WALDEN Nora MAURIN Olivier HAY Nikolai M SHUSHKOV Philip MALÍK MANDÁKOVÁ Terezie SCHRANZ M Eric THULIN Mats WINDHAM Michael D RESETNIK Ivana SPANIEL Stanislav LY Elfy PIRES J Chris HARKESS Alex NEUFFER Barbara VOGT Robert BRAUCHLER Christian RAINER Heimo JANSSENS Steven B SCHMULL Michaela FORREST Alan GUGGISBERG Alessia ZMARZTY Sue LEPSCHI Brendan J SCARLETT Neville STAUFFER Fred W SCHONBERGER Ines HEENAN Peter BAKER William J FOREST Felix MUMMENHOFF Klaus LENS Frederic
Year of publication	2023
Type	Article in Periodical
Magazine / Source	Current Biology
MU Faculty or unit	Central European Institute of Technology
Citation
Web	https://www.sciencedirect.com/science/article/pii/S0960982223010692?via%3Dihub
Doi	http://dx.doi.org/10.1016/j.cub.2023.08.026
Keywords	MULTIPLE SEQUENCE ALIGNMENT; MOLECULAR SYSTEMATICS; PENALIZED LIKELIHOOD; EVOLUTION; DIVERSIFICATION; BIOGEOGRAPHY; ARABIDOPSIS; PLANT DIPLOIDIZATION; TRANSITION
Description	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 (Bras-sicaceae 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 eval-uate 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 moder-ate. 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.
Related projects:	Unlocking evolutionary secrets of false flax and its relatives The origin and evolution of apomixis-related chromosomes in Boechera (Brassicaceae)