title: Towards a comprehensive phylogeny of the large temperate genus Pedicularis (Orobanchaceae), with an emphasis on species from the Himalaya-Hengduan Mountains.
abstract: BACKGROUND
  Striking interspecific variations in floral traits of the large temperate genus Pedicularis have given rise to controversies concerning infra-generic classifications. To date, phylogenetic relationships within the genus have not been well resolved. The main goal of this study is to construct a backbone phylogeny of Pedicularis, with extensive sampling of species from the Himalaya-Hengduan Mountains. Phylogenetic analyses included 257 species, representing all 13 informal groups and 104 out of 130 series in the classification system of Tsoong, using sequences of the nuclear ribosomal internal transcribed spacer (nrITS) and three plastid regions (matK, rbcL and trnL-F). Bayesian inference and maximum likelihood methods were applied in separate and combined analyses of these datasets.
  
  
  RESULTS
  Thirteen major clades are resolved with strong support, although the backbone of the tree is poorly resolved. There is little consensus between the phylogenetic tree and Tsoong's classification of Pedicularis. Only two of the 13 groups (15.4 %), and 19 of the 56 series (33.9 %) with more than one sampled species were found to be strictly monophyletic. Most opposite-/whorled-leaved species fall into a single clade, i.e. clade 1, while alternate leaves species occur in the remaining 12 clades. Excluding the widespread P. verticillata in clade 1, species from Europe and North America fall into clades 6-8.
  
  
  CONCLUSIONS
  Our results suggest that combinations of morphological and geographic characters associated with strongly supported clades are needed to elucidate a comprehensive global phylogeny of Pedicularis. Alternate leaves are inferred to be plesiomorphic in Pedicularis, with multiple transitions to opposite/whorled phyllotaxy. Alternate-leaved species show high diversity in plant habit and floral forms. In the Himalaya-Hengduan Mountains, geographical barriers may have facilitated diversification of species with long corolla tubes, and the reproductive advantages of beakless galeas in opposite-/whorled-leaved species may boost speciation at high altitude.
authors.affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China. yuwenbin@xtbg.ac.cn.|Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, PR China. yuwenbin@xtbg.ac.cn.
authors.forename: Wen-Bin
authors.initials: WB
authors.lastname: Yu
authors.affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China. liuminlu@mail.kib.ac.cn.|Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, PR China. liuminlu@mail.kib.ac.cn.
authors.forename: Min-Lu
authors.initials: ML
authors.lastname: Liu
authors.affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China. wanghong@mail.kib.ac.cn.|Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China. wanghong@mail.kib.ac.cn.
authors.forename: Hong
authors.initials: H
authors.lastname: Wang
authors.affiliation: Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, Scotland, UK. r.mill@rbge.ac.uk.
authors.forename: Robert R
authors.initials: RR
authors.lastname: Mill
authors.affiliation: Department of Botany, Field Museum of Natural History, Chicago, IL, 60605, USA. rree@fieldmuseum.org.
authors.forename: Richard H
authors.initials: RH
authors.lastname: Ree
authors.affiliation: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China. jbyang@mail.kib.ac.cn.
authors.forename: Jun-Bo
authors.initials: JB
authors.lastname: Yang
authors.affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China. dzl@mail.kib.ac.cn.|Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China. dzl@mail.kib.ac.cn.
authors.forename: De-Zhu
authors.initials: DZ
authors.lastname: Li
mesh_terms: D002467:Cell Nucleus / Q000235:genetics / Q000378:metabolism; D002681:China; D060365:Chloroplast Proteins / Q000235:genetics / Q000378:metabolism; D032262:Pedicularis / Q000033:anatomy & histology / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D060365:Chloroplast Proteins; D010940:Plant Proteins