Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)

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	Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)
	Ma, Peng-Fei 1,2,3; Zhang, Yu-Xiao 1,2; Zeng, Chun-Xia 2; Guo, Zhen-Hua2 ; Li, De-Zhu1,2
刊名	SYSTEMATIC BIOLOGY
	2014-11-01
卷号	63 期号:6 页码:933-950
关键词	Branch length chloroplast phylogenomics data partitioning low sequence divergence sampling temperate woody bamboos
ISSN号	1063-5157
通讯作者	Li,DZ (reprint author),Chinese Acad Sci,Kunming Inst Bot,132 Lanhei Rd,Kunming 650201,Yunnan,Peoples R China. ; dzl@mail.kib.ac.cn
产权排序	第一
英文摘要	The temperate woody bamboos constitute a distinct tribe Arundinarieae (Poaceae: Bambusoideae) with high species diversity. Estimating phylogenetic relationships among the 11 major lineages of Arundinarieae has been particularly difficult, owing to a possible rapid radiation and the extremely low rate of sequence divergence. Here, we explore the use of chloroplast genome sequencing for phylogenetic inference. We sampled 25 species (22 temperate bamboos and 3 outgroups) for the complete genome representing eight major lineages of Arundinarieae in an attempt to resolve backbone relationships. Phylogenetic analyses of coding versus noncoding sequences, and of different regions of the genome (large single copy and small single copy, and inverted repeat regions) yielded no well-supported contradicting topologies but potential incongruence was found between the coding and noncoding sequences. The use of various data partitioning schemes in analysis of the complete sequences resulted in nearly identical topologies and node support values, although the partitioning schemes were decisively different from each other as to the fit to the data. Our full genomic data set substantially increased resolution along the backbone and provided strong support for most relationships despite the very short internodes and long branches in the tree. The inferred relationships were also robust to potential confounding factors (e. g., long-branch attraction) and received support from independent indels in the genome. We then added taxa from the three Arundinarieae lineages that were not included in the full-genome data set; each of these were sampled for more than 50% genome sequences. The resulting trees not only corroborated the reconstructed deep-level relationships but also largely resolved the phylogenetic placements of these three additional lineages. Furthermore, adding 129 additional taxa sampled for only eight chloroplast loci to the combined data set yielded almost identical relationships, albeit with low support values. We believe that the inferred phylogeny is robust to taxon sampling. Having resolved the deep-level relationships of Arundinarieae, we illuminate how chloroplast phylogenomics can be used for elucidating difficult phylogeny at low taxonomic levels in intractable plant groups.
学科主题	Evolutionary Biology
类目[WOS]	Evolutionary Biology
研究领域[WOS]	Evolutionary Biology
关键词[WOS]	ENIGMATIC RELATIONSHIPS ; BAYESIAN PHYLOGENETICS ; EVOLUTIONARY HISTORY ; C-4 PHOTOSYNTHESIS ; PLASTID GENOMES ; GRASSES POACEAE ; TREE SELECTION ; WOODY BAMBOOS ; MIXED MODELS ; NUCLEAR LOCI
收录类别	SCI
资助信息	NSFC [81373288]; Natural Science Foundation of Yunnan Province [2008CD158]; Western Doctoral Foundation of Chinese Academy of Sciences; Foundation of State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences [P2008ZZ23, P2010ZZ14]; Cooperative Project of Guangdong Province; CAS [2009B091300135]
语种	英语
WOS记录号	WOS:000344695900006
公开日期	2015-01-20
内容类型	期刊论文
源URL	[http://ir.kib.ac.cn/handle/151853/18515]
专题	昆明植物研究所_中国西南野生生物种质资源库
作者单位	1.Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China 2.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Plant Germplasm & Genom Ctr, Kunming 650201, Yunnan, Peoples R China 3.Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650201, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Ma, Peng-Fei,Zhang, Yu-Xiao,Zeng, Chun-Xia,et al. Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)[J]. SYSTEMATIC BIOLOGY,2014,63(6):933-950.
APA	Ma, Peng-Fei,Zhang, Yu-Xiao,Zeng, Chun-Xia,Guo, Zhen-Hua,&Li, De-Zhu.(2014).Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae).SYSTEMATIC BIOLOGY,63(6),933-950.
MLA	Ma, Peng-Fei,et al."Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)".SYSTEMATIC BIOLOGY 63.6(2014):933-950.