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Incongruence between Nuclear and Chloroplast DNA Phylogenies in Pedicularis Section Cyathophora (Orobanchaceae)
source:     author:YU Wenbin     2013-09-27

Pedicularis (Orobanchaceae) comprises approximately 600-800 species, one of the largest genera of flowering plants in the north temperate zone. About two thirds of these species are confined to the region of the Hengduan Mountains in southwestern China, which represents one of the main centers of species diversity and endemism for this genus. Pedicularis section Cyathophora is characterized by the bases of whorled leaves and/or bracts that are dilated and fused together to form a cup-like structure around the stem at each node. Despite consisting of seven species (including one questionable species) and restricted to the eastern Himalaya-Hengduan Mountains, section Cyathophora is highly diverse in floral shape, including all four general corolla types. This section is a monophyletic subgeneric taxa supported by molecular phylogenies, however, relationships among its members are poorly understood.

 Recently, Dr. YU Wenbin advised by Profs. LI Dezhu and WANG Hong, from Kunming institute of botany, generated nuclear and chloroplast datasets to reconstruct a comprehensive phylogeny of section Cyathophora, and to compare phylogenetic incongruence between nuclear and chloroplast datasets. Sixty-seven accessions belonging to section Cyathophora and 9 species for other Pedicularis were sampled, and one nuclear gene (nrITS) and four chloroplast genes (matK, rbcL, trnH-psbA and trnL-F) were sequenced. Phylogenetic analyses show that the topologies and networks inferred from nrITS and the concatenated chloroplast datasets were incongruent, and the nrITS phylogenies and network agreed with the morphology-based taxonomy to some degree. The chloroplast genome of two Sichuan samples of P. cyathophylloides (E4 and E5) may show introgression from an ancestor of P. cyathophylla. Neither the nrITS dataset nor the concatenated chloroplast dataset were able to adequately resolve relationships among species in the series Reges; this is most likely due to incomplete lineage sorting and/or introgression/hybridization. The nrITS phylogeny indicates the beakless (toothed and toothless) and beaked galeas may have evolved independently within section Cyathophora, and the chloroplast phylogeny reveals that the long corolla tube with beaked galea is derived from the short one.

 This work has been published in the journal PLoS ONE on September 19, 2013, entitled “Incongruence between Nuclear and Chloroplast DNA Phylogenies in Pedicularis Section Cyathophora (Orobanchaceae)” (http://dx.plos.org/10.1371/journal.pone.007482).8

 This study is supported by grants from the National Natural Science Foundation of China (31200185), the West Light Foundation of the Chinese Academy of Sciences, the National High-tech Research & Development Program of China (2012AA021801), the National Science and Technology on Basic Research Program (2013FY112600), the Key Research Program of the Chinese Academy of Sciences (KJZD-EW-L07), the Large-Scale Scientific Facilities of the Chinese Academy of Sciences (2009-LSF-GBOWS-01), and the National Key Basic Research Program of China (2014CB954100).

Figure 1. Four general corolla types in Pedicularis section Cyathophora

Figure 2. Phylogenies of Pedicularis section Cyathophora inferred from Bayesian, maximum likelihood and maximum parsimony methods using nrITS (A) and the concatenated chloroplast (B) datasets.

Figure 3. Geographical information for studied samples of Pedicularis section Cyathophora

Figure 4. Neighbor-net analysis of Pedicularis section Cyathophora using nrITS (A) and the concatenated chloroplast (B) datasets.



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