Nuclear and plastid DNA phylogeny of tribe Cardueae (Compositae) with Hyb-Seq data : A new subtribal classification and a temporal diversification framework

Show full item record



Permalink

http://hdl.handle.net/10138/318086

Citation

Cardueae Radiations Grp 2019 , ' Nuclear and plastid DNA phylogeny of tribe Cardueae (Compositae) with Hyb-Seq data : A new subtribal classification and a temporal diversification framework ' , Molecular Phylogenetics and Evolution , vol. 137 , pp. 313-332 . https://doi.org/10.1016/j.ympev.2019.05.001

Title: Nuclear and plastid DNA phylogeny of tribe Cardueae (Compositae) with Hyb-Seq data : A new subtribal classification and a temporal diversification framework
Author: Herrando-Moraira, Sonia; Antonio Calleja, Juan; Galbany-Casals, Merce; Garcia-Jacas, Nuria; Liu, Jian-Quan; Lopez-Alvarado, Javier; Lopez-Pujol, Jordi; Mandel, Jennifer R.; Masso, Sergi; Montes-Moreno, Noemi; Roquet, Cristina; Saez, Llorenc; Sennikov, Alexander; Susanna, Alfonso; Vilatersana, Roser
Contributor: University of Helsinki, Botany
Date: 2019-08
Number of pages: 20
Belongs to series: Molecular Phylogenetics and Evolution
ISSN: 1055-7903
URI: http://hdl.handle.net/10138/318086
Abstract: 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.
Subject: Asteraceae
COS targets
Subtribes
Systematics
Phylogenomics
Target enrichment
PENALIZED LIKELIHOOD
EVOLUTIONARY HISTORY
MAXIMUM-LIKELIHOOD
TAXONOMIC LEVELS
ASTERACEAE
RESOLUTION
ALIGNMENT
EOCENE
RECONSTRUCTION
SYSTEMATICS
1181 Ecology, evolutionary biology
Rights:
Full text embargoed until: 2020-08-01


Files in this item

Files Size Format View

Embargo on files ends: 2020-08-01

This item appears in the following Collection(s)

Show full item record