Phylogeny of Rosa sections Chinenses and Synstylae (Rosaceae) based on chloroplast and nuclear markers Zhang-Ming Zhu a,b , Xin-Fen Gao a,⇑ , Marie Fougère-Danezan a,c a Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China b University of Chinese Academy of Sciences, Beijing 100049, China c Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China article info Article history: Received 31 October 2014 Revised 4 March 2015 Accepted 14 March 2015 Available online 23 March 2015 Keywords: Rosa Section Chinenses Section Synstylae Phylogeny Incongruence Hybridization abstract Rosa sections Chinenses and Synstylae contain approximately 39 wild species mainly distributed in East Asia and are closely related according to previous studies. But the specific relationships within these two sections were still obscure due to limited sampling, low genetic variation of molecular markers, and complex evolutionary histories. In this study, we used four chloroplast (ndhC-trnV, ndhF-rpl32, ndhJ-trnF and psbJ-petA) and two nuclear (ribosomal ITS and GAPDH) markers with an extensive geo- graphic and taxonomic sampling to explore their evolutionary history. Our phylogenetic analyses sug- gested that Rosa sections Chinenses and Synstylae defined in traditional taxonomic system are not monophyletic and close to sections Caninae and Gallicanae. Additionally, our results showed incongru- ence between chloroplast and nuclear markers, and the patterns of incongruence might be due to ancient hybridization (genetic introgression). One putative hybrid species and three samples identified as inter- specific hybrids are further discussed in terms of topological incongruence, biological characters and dis- tribution patterns. Ó 2015 Elsevier Inc. All rights reserved. 1. Introduction Hybridization has long been recognized as an important driving force in plant evolution (Abbott, 1992; Mallet, 2007; Paun et al., 2009; Rieseberg, 1995, 1997), which can lead to high intraspecific genetic diversity, creation of new species or ecotypes, and reticu- late evolution (Anderson, 1948; Linder and Rieseberg, 2004; Whitham et al., 1994). As a result, it is particularly challenging to reconstruct species relationships for groups including hybrids. In the genus Rosa L. (Rosaceae), interspecific hybrids are easily formed, which have contributed substantially to the diversity in this genus (Atienza et al., 2005; Rehder, 1940; Wissemann, 2003). Many hybridization events have been reported in wild roses (Atienza et al., 2005; Joly et al., 2006; Matthews, 1920; Schanzer and Kutlunina, 2010). The whole section Caninae seems to be of hybrid origin (Fougère-Danezan et al., 2015; Ritz et al., 2005; Wissemann, 1999). Some species of Rosa sects. Rosa and Synstylae were also shown to have undergone hybridization during their evolutionary histories (Joly et al., 2006; Ohba et al., 2000). Indeed, hybridization has been recognized as one of the major difficulties in the taxonomy of roses even since the early times (Crépin, 1889; Linnaeus, 1753). The genus Rosa comprises about 150–200 species widely dis- tributed in the temperate and subtropical regions of the northern hemisphere (Ku and Robertson, 2003; Yü et al., 1985). The widely adopted taxonomic system built by Rehder (1940) divided Rosa species into four subgenera, i.e., Hesperhodos Cockerell, Hulthemia (Dumort.) Focke, Platyrhodon (Hurst) Rehder and Rosa. The first three subgenera contain only one or two species, while species from the subgenus Rosa are further divided into ten sections, i.e., Banksiae Lindl., Bracteatae Thory, Caninae (DC.) Ser., Carolinae Crép., Cinnamomeae (DC.) Ser., Gallicanae (DC.) Ser., Indicae Thory, Laevigatae Thory, Pimpinellifoliae (DC.) Ser., and Synstylae DC. We use R. sect. Chinenses (DC.) Ser. in this study instead of R. sect. Indicae since the former is the oldest valid name while the latter is a synonym (Seringe, 1818; Thory, 1820). Because R. sect. Cinnamomeae includes the type species (R. cinnamomea L.) of the genus (Barrie, 2006; Jarvis, 1992), the section name Cinnamomeae is invalid and should be replaced by the autonym (R. sect. Rosa; Art. 22.1, McNeill et al., 2012). So we use R. sect. Rosa instead of R. sect. Cinnamomeae in this study. Many attempts were made to reconstruct the phylogeny of this genus, most of which suggested that the divisions of most subgen- era and sections based on morphology were artificial (Bruneau http://dx.doi.org/10.1016/j.ympev.2015.03.014 1055-7903/Ó 2015 Elsevier Inc. All rights reserved. ⇑ Corresponding author. E-mail address: xfgao@cib.ac.cn (X.-F. Gao). Molecular Phylogenetics and Evolution 87 (2015) 50–64 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev