Nuclear and plastid DNA phylogeny of tribe Cardueae (Compositae) with Hyb-Seq data : A new subtribal classification and a temporal diversification framework
Herrando-Moraira, Sonia (Institut Botànic de Barcelona)
Calleja, Juan Antonio (Universitat Autònoma de Barcelona. Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia)
Galbany-Casals, Mercè (Universitat Autònoma de Barcelona. Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia)
Garcia-Jacas, Núria (Institut Botànic de Barcelona)
Liu, Jian-Quan (Key Sichuan University)
López-Alvarado, Javier (Universitat Autònoma de Barcelona. Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia)
López-Pujol, Jordi (Institut Botànic de Barcelona)
Mandel, Jennifer R. (University of Memphis. Department of Biological Sciences)
Massó, Sergi (Universitat Autònoma de Barcelona. Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia)
Montes-Moreno, Noemí (Institut Botànic de Barcelona)
Roquet, Cristina (Universitat Autònoma de Barcelona. Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia)
Sáez, Llorenç (Universitat Autònoma de Barcelona. Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia)
Sennikov, Alexander N. (Finnish Museum of Natural History)
Susanna, Alfonso (Institut Botànic de Barcelona)
Vilatersana, Roser (Institut Botànic de Barcelona)

Data:	2019
Resum:	Classification of tribe Cardueae in natural subtribes has always been a challenge due to the lack of support of some critical branches in previous phylogenies based on traditional Sanger markers. With the aim to propose a new subtribal delimitation, we applied a Hyb-Seq approach to a set of 76 Cardueae species representing all subtribes and informal groups defined in the tribe, targeting 1061 nuclear conserved orthology loci (COS) designed for Compositae and obtaining chloroplast coding regions as by-product of off-target reads. For the extraction of the target nuclear data, we used two strategies, PHYLUCE and HybPiper, and 776 and 1055 COS loci were recovered with each of them, respectively. Additionally, 87 chloroplast genes were assembled and annotated. With three datasets, phylogenetic relationships were reconstructed using both concatenation and coalescent approaches. Phylogenetic analyses of the nuclear datasets fully resolved virtually all nodes with very high support. Nuclear and plastid tree topologies are mostly congruent with a very limited number of incongruent nodes. Based on the well-solved phylogenies obtained, we propose a new taxonomic scheme of 12 monophyletic and morphologically consistent subtribes: Carlininae, Cardopatiinae, Echinopsinae, Dipterocominae (new), Xerantheminae (new), Berardiinae (new), Staehelininae (new), Onopordinae (new), Carduinae (redelimited), Arctiinae (new), Saussureinae (new), and Centaureinae. In addition, we further updated the temporal framework for origin and diversification of these subtribes. Our results highlight the power of Hyb-Seq over Sanger sequencing of a few DNA markers in solving phylogenetic relationships of traditionally difficult groups.
Ajuts:	Agència de Gestió d'Ajuts Universitaris i de Recerca 2017/SGR-1116 Ministerio de Ciencia e Innovación CGL2015-66703-P
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, i la comunicació pública de l'obra, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original. No es permet la creació d'obres derivades.
Llengua:	Anglès
Document:	Article ; recerca ; Versió acceptada per publicar
Publicat a:	Molecular Phylogenetics and Evolution, Vol. 137 (August 2019) , p. 313-332, ISSN 1095-9513

DOI: 10.1016/j.ympev.2019.05.001

Postprint 60 p, 9.3 MB

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