Using nuclear loci and allelic variation to disentangle the phylogeny of Phyllostachys (Poaceae, Bambusoideae)

doi:10.1016/j.ympev.2019.05.011

	Using nuclear loci and allelic variation to disentangle the phylogeny of Phyllostachys (Poaceae, Bambusoideae)
	Zhang, Li-Na 1,2; Ma, Peng-Fei 1; Zhang, Yu-Xiao 3; Zeng, Chun-Xia 1; Zhao, Lei 1; Li, De-Zhu1
通讯作者	Li, De-Zhu(dzl@mail.kib.ac.cn)
	2019-08-01
发表期刊	MOLECULAR PHYLOGENETICS AND EVOLUTION
ISSN	1055-7903
卷号	137 页码:222-235
摘要	With the development of sequencing technologies, the use of multiple nuclear genes has become conventional for resolving difficult phylogenies. However, this technique also presents challenges due to gene-tree discordance, as a result of incomplete lineage sorting (ILS) and reticulate evolution. Although alleles can show sequence variation within individuals, which contain information regarding the evolution of organisms, they continue to be ignored in almost all phylogenetic analyses using randomly phased genome sequences. Here, we tried to incorporate alleles from multiple nuclear loci to study the phylogeny of the economically important bamboo genus Phyllostachys (Poaceae, Bambusoideae). Obtaining a total of 3926 sequences, we documented extensive allelic variation for 61 genes from 39 sampled species. Using datasets consisting of selected alleles, we demonstrated substantial discordance among phylogenetic relationships inferred from different alleles, as well as between concatenation and coalescent methods. Furthermore, ILS and hybridization were suggested to be underlying causes of the discordant phylogenetic signals. Taking these possible causes for conflicting phylogenetic results into consideration, we recovered the monophyly of Phyllostachys and its two morphology-defined sections. Our study also suggests that alleles deserve more attention in phylogenetic studies, since ignoring them can yield highly supported but spurious phylogenies. Meanwhile, alleles are helpful for unraveling complex evolutionary processes, particularly hybridization.
关键词	Alleles Bamboo Hybridization Incomplete lineage sorting Monophyly Phylogenetic inference
DOI	10.1016/j.ympev.2019.05.011
收录类别	SCI
语种	英语
WOS记录号	WOS:000472499000019
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/67288
专题	中国西南野生生物种质资源库
通讯作者	Li, De-Zhu
作者单位	1.Chinese Acad Sci, Kunming Inst Bot, Gerrnplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China 2.Fujian Agr & Forestry Univ, Coll Life Sci, Fuzhou 350002, Fujian, Peoples R China 3.Southwest Forestry Univ, Yunnan Acad Biodivers, Kunming 650224, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Li-Na,Ma, Peng-Fei,Zhang, Yu-Xiao,et al. Using nuclear loci and allelic variation to disentangle the phylogeny of Phyllostachys (Poaceae, Bambusoideae)[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2019,137:222-235.
APA	Zhang, Li-Na,Ma, Peng-Fei,Zhang, Yu-Xiao,Zeng, Chun-Xia,Zhao, Lei,&Li, De-Zhu.(2019).Using nuclear loci and allelic variation to disentangle the phylogeny of Phyllostachys (Poaceae, Bambusoideae).MOLECULAR PHYLOGENETICS AND EVOLUTION,137,222-235.
MLA	Zhang, Li-Na,et al."Using nuclear loci and allelic variation to disentangle the phylogeny of Phyllostachys (Poaceae, Bambusoideae)".MOLECULAR PHYLOGENETICS AND EVOLUTION 137(2019):222-235.

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