Nuclear and Plastid DNA Phylogeny of the Tribe Cardueae (Compositae

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Nuclear and Plastid DNA Phylogeny of the Tribe Cardueae (Compositae 1 Nuclear and plastid DNA phylogeny of the tribe Cardueae 2 (Compositae) with Hyb-Seq data: A new subtribal classification and a 3 temporal framework for the origin of the tribe and the subtribes 4 5 Sonia Herrando-Morairaa,*, Juan Antonio Callejab, Mercè Galbany-Casalsb, Núria Garcia-Jacasa, Jian- 6 Quan Liuc, Javier López-Alvaradob, Jordi López-Pujola, Jennifer R. Mandeld, Noemí Montes-Morenoa, 7 Cristina Roquetb,e, Llorenç Sáezb, Alexander Sennikovf, Alfonso Susannaa, Roser Vilatersanaa 8 9 a Botanic Institute of Barcelona (IBB, CSIC-ICUB), Pg. del Migdia, s.n., 08038 Barcelona, Spain 10 b Systematics and Evolution of Vascular Plants (UAB) – Associated Unit to CSIC, Departament de 11 Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de 12 Barcelona, ES-08193 Bellaterra, Spain 13 c Key Laboratory for Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 14 Chengdu, China 15 d Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA 16 e Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA (Laboratoire d’Ecologie Alpine), FR- 17 38000 Grenoble, France 18 f Botanical Museum, Finnish Museum of Natural History, PO Box 7, FI-00014 University of Helsinki, 19 Finland; and Herbarium, Komarov Botanical Institute of Russian Academy of Sciences, Prof. Popov str. 20 2, 197376 St. Petersburg, Russia 21 22 *Corresponding author at: Botanic Institute of Barcelona (IBB, CSIC-ICUB), Pg. del Migdia, s. n., ES- 23 08038 Barcelona, Spain. E-mail address: [email protected] (S. Herrando-Moraira). 24 25 Abstract 26 Classification of the tribe Cardueae in natural subtribes has always been a challenge due to the lack of 27 support of some critical branches in previous phylogenies based on traditional Sanger markers. With the 28 aim to propose a new subtribal delimitation, we applied a Hyb-Seq approach to a set of 76 Cardueae 29 species representing all the subtribes and informal groups defined in the tribe, targeting 1061 nuclear 30 conserved orthology loci (COS) designed for Compositae and obtaining chloroplast coding regions as by- 31 product of off-target reads. For the extraction of target nuclear data, we used two strategies, PHYLUCE 32 and HybPiper, and 776 and 1055 COS loci were recovered with each of them, respectively. Additionally, 33 87 chloroplast genes were assembled and annotated. With the three datasets, phylogenetic relationships 34 within the tribe were reconstructed under approaches of concatenation (using supermatrices as input for 35 maximum likelihood analysis with RAxML) and coalescence (species tree estimated with ASTRAL 36 based on the individual gene trees of each COS locus). The phylogenetic analyses of the nuclear datasets 37 fully resolved virtually all nodes with very high support. Although nuclear and plastid tree topologies are 38 highly congruent, they still present some incongruences, which are shortly discussed. On the basis of the 39 phylogenies obtained, we propose a new taxonomic scheme of 12 monophyletic and morphologically 40 consistent subtribes: Carlininae, Cardopatiinae, Echinopsinae, Dipterocominae (new), Xerantheminae 41 (new), Berardiinae (new), Staehelininae (new), Onopordinae (new), Carduinae (redelimited), Arctiinae 42 (new), Saussureinae (new), and Centaureinae. Another main key result of the study was the high 43 resolution recovered at the backbone of the Cardueae tree, which led to obtain better inter-subtribal 44 relationships. Using as tree base the nuclear HybPiper phylogeny, we updated the temporal framework for 45 the origin and diversification of the tribe and subtribes. Overall, the power of Hyb-Seq is demonstrated to 46 solve relationships traditionally suggested by morphology but never recovered with support using Sanger 47 sequencing of a few DNA markers. 48 49 Keywords 50 Asteraceae 51 COS targets 52 Subtribes 53 Systematics 54 Phylogenomics 55 Target enrichment 56 57 58 59 1. Introduction 60 61 The Cardueae is one of the largest tribes of the 43 described in the Compositae (Asteraceae; Funk et al., 62 2009), with almost 10% of the species of the whole family: 2400 species in 73 genera (Susanna and 63 Garcia-Jacas, 2009). The tribe belongs to the subfamily Carduoideae, which is composed by four tribes 64 (Panero and Funk, 2008; Ortiz et al., 2009): Dicomeae (97 spp.), Tarchonantheae (13 spp.), 65 Oldenburgieae (4 spp.), and Cardueae, the latter representing the 95% of the subfamily’s diversity 66 (Susanna and Garcia-Jacas, 2009). The Carduoideae is a very successful evolutionary lineage within 67 Compositae, which was estimated by Panero and Crozier (2016) to have the second highest 68 diversification rate in the family and a moderate rate of extinction. The number of species is not uniform 69 across the genera of the tribe Cardueae, being six of them highly diversified (ca. 200–600 spp.) and with a 70 high endemism rate (Carduus, Cirsium, Centaurea, Cousinia, Jurinea, and Saussurea), while, on the 71 other extreme, 22 (ca. 30%) are monotypic. Geographically, the tribe is distributed mainly in the 72 Mediterranean and the Irano-Turanian regions, but it is reported from all continents except the Antarctica. 73 The ecosystems where the Cardueae species inhabit are very variable, e.g. Mediterranean landscapes, 74 steppes, semiarid areas, deserts, alpine meadows, or tropical savannahs (Susanna and Garcia-Jacas, 2009). 75 Indeed, in many aspects the tribe Cardueae is an extremely heterogeneous group in terms of habit 76 (perennial, biennial, monocarpic or annual herbs, shrubs, treelets, often spiny), karyology (high variability 77 in chromosome numbers from x=6 to x=18, frequent disploidy), or pollen structure (caveate or ecaveate, 78 smooth, scabrate, or spiny). This complexity summed to its high diversity have greatly contributed to the 79 turbulent taxonomic history of Cardueae at several ranks, e.g. tribal and subtribal (see Table 1 for a 80 historical overview) or even misclassifications of some genera in different tribes or subtribes (see 81 examples in Table 2). 82 In the first tribal classification of the family, Cassini (1819) divided the present Cardueae into three 83 tribes: Echinopseae, Carlineae, and Cardueae, the latter comprising the subtribes Carduinae and 84 Centaureinae. Years later, Bentham (1873) and Hoffmann (1894) proposed grouping the three former 85 tribes in a single tribe Cardueae, with four subtribes: Carlininae Dumort., Echinopsinae [“Echinopinae”] 86 Dumort., Carduinae Cass., and Centaureinae Dumort. This conservative approach was accepted over long 87 time, until Wagenitz (1976) reinstated the tribe Echinopseae. Soon after, Dittrich (1977) returned to 88 Cassini's earlier views, proposing the restoration of tribes Echinopseae, Carlineae, and Cardueae. Bremer 89 (1994) favored the conservative classification of a single tribe Cardueae, which is nowadays generally 90 accepted (Susanna and Garcia-Jacas, 2007, 2009), with the recent reinstauration of the subtribe 91 Cardopatiinae (Susanna et al., 2006). 92 Not surprisingly, Carlininae and Echinopsinae, two of the two basalmost subtribes in molecular 93 phylogenies, have been considered at some time as independent tribes, mainly due to their clear 94 diagnostic characters with respect to the rest of the Cardueae assembly (Susanna and Garcia-Jacas, 2009). 95 However, the Cardueae are morphologically consistent as a whole entity at the tribal level, sharing a 96 unique synapomorphic morphological character within the Compositae: style with a papillose-pilose 97 thickening below the branches and the stigmatic areas confined to the inner surface (Susanna and Garcia- 98 Jacas, 2009). Additionally, the tribe Cardueae has also been broadly confirmed empirically as 99 monophyletic, first by cladistic analyses based on morphology (Bremer, 1987, 1994; Karis et al., 1992), 100 and later by molecular phylogenies (Jansen et al., 1990, 1991; Kim et al., 1992; Susanna et al., 1995, 101 2006; Garcia-Jacas et al., 2002; Barres et al., 2013). 102 In the most recent and accepted treatments (Susanna et al., 2006; Susanna and Garcia-Jacas, 2007, 103 2009), the authors pointed out that four subtribes are natural groups with clear limits (Cardopatiinae, 104 Carlininae, Centaureinae, and Echinopsinae); however, subtribe Carduinae is an unnatural, artificial, and 105 problematic group. The Carduinae have been a dumping ground of genera that do not fit in any of the 106 other subtribes and totals 1700 species, near 70% of the whole tribe diversity (Susanna and Garcia-Jacas, 107 2007). The fact that the group is a questionable and heterogeneous assemblage of genera was also 108 reflected in several phylogenetic studies, which have reported the subtribe as paraphyletic (Susanna et al., 109 1995, 2006; Häffner and Hellwig, 1999; Garcia-Jacas et al., 2002; Barres et al., 2013). The alternate 110 solution of combining subtribes Carduinae and Centaureinae in one enormous subtribe was discarded, 111 owing to the impractical constitution of a huge subtribe encompassing 2300 species and 90% of the 112 species of the whole tribe (Susanna and Garcia-Jacas, 2007). 113 With the intention of fragmenting subtribe Carduinae, some informal morphological groups have 114 been described within it (Susanna and Garcia-Jacas, 2007), which could on the long run be considered 115 subtribes for a more natural classification: “[the alternative is] splitting present Carduinae in at least seven 116 new subtribes (many of them presently unsupported): Xerantheminae,
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