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Using nuclear loci and allelic variation to disentangle the phylogeny of Phyllostachys (Poaceae, Bambusoideae)
Zhang, Li-Na1,2; Ma, Peng-Fei1; Zhang, Yu-Xiao3; Zeng, Chun-Xia1; Zhao, Lei1; Li, De-Zhu1
Corresponding AuthorLi, De-Zhu(
AbstractWith 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.
KeywordAlleles Bamboo Hybridization Incomplete lineage sorting Monophyly Phylogenetic inference
Indexed BySCI
WOS IDWOS:000472499000019
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Document Type期刊论文
Corresponding AuthorLi, De-Zhu
Affiliation1.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
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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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