title: The monophyly of Chimonocalamus and conflicting gene trees in Arundinarieae (Poaceae: Bambusoideae) inferred from four plastid and two nuclear markers.
abstract: Arundinarieae is not only a taxonomically difficult group of bamboos, but also a troublesome one in molecular phylogenetics. In this study, the phylogeny of 50 species in Arundinarieae with an emphasis on Chimonocalamus was reconstructed, using four plastid regions (rpl32-trnL, trnT-trnL, rps16-trnQ and trnC-rpoB) and two nuclear genes (GBSSI and LEAFY). The plastid phylogeny was largely consistent with the previous studies, except that Ampelocalamus calcareus was newly recovered as lineage XI. The nuclear phylogeny of LEAFY had better resolution than the one of GBSSI. The close relationships among Ampelocalamus, Drepanostachyum and Himalayacalamus were retrieved by the nuclear datasets. Alpine Bashania, Chimonocalamus, Thamnocalamus, and species currently placed in Fargesia and Yushania formed a clade in the LEAFY and combined nuclear phylogenies. Some of the gene tree disparities revealed in previous studies were reconfirmed. Chimonocalamus was recovered as monophyletic by combining the nuclear genes, but as polyphyletic in plastid analyses. Insufficient informative characters, hybridization, plastid capture or incomplete plastid lineage sorting could be responsible for the incongruent phylogenetic positions of some species of Chimonocalamus.
authors.affiliation: Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
authors.forename: Hong-Mei
authors.initials: HM
authors.lastname: Yang
authors.forename: Yu-Xiao
authors.initials: YX
authors.lastname: Zhang
authors.forename: Jun-Bo
authors.initials: JB
authors.lastname: Yang
authors.forename: De-Zhu
authors.initials: DZ
authors.lastname: Li
mesh_terms: D001499:Bayes Theorem; D002467:Cell Nucleus / Q000235:genetics; D018628:Gene Dosage; D017343:Genes, Plant; D005819:Genetic Markers; D016013:Likelihood Functions; D058977:Molecular Sequence Annotation; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D018087:Plastids / Q000235:genetics*; D006109:Poaceae / Q000145:classification / Q000201:enzymology / Q000235:genetics*; D013214:Starch Synthase / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics
chemical_list: D005819:Genetic Markers; D010940:Plant Proteins; D014157:Transcription Factors; C434607:granule-bound starch synthase I; D013214:Starch Synthase