Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae)

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	Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae)
	Qu, Xiao-Jian1,2 ; Jin, Jian-Jun 1,2; Chaw, Shu-Miaw 3; Li, De-Zhu1,2 ; Yi, Ting-Shuang1
刊名	SCIENTIFIC REPORTS
	2017-01-25
卷号	7
英文摘要	Long-branch attraction (LBA) is a major obstacle in phylogenetic reconstruction. The phylogenetic relationships among Juniperus (J), Cupressus (C) and the Hesperocyparis-Callitropsis-Xanthocyparis (HCX) subclades of Cupressoideae are controversial. Our initial analyses of plastid protein-coding gene matrix revealed both J and C with much longer stem branches than those of HCX, so their sister relationships may be attributed to LBA. We used multiple measures including data filtering and modifying, evolutionary model selection and coalescent phylogenetic reconstruction to alleviate the LBA artifact. Data filtering by strictly removing unreliable aligned regions and removing substitution saturation genes and rapidly evolving sites could significantly reduce branch lengths of subclades J and C and recovered a relationship of J (C, HCX). In addition, using coalescent phylogenetic reconstruction could elucidate the LBA artifact and recovered J (C, HCX). However, some valid methods for other taxa were inefficient in alleviating the LBA artifact in J-C-HCX. Different strategies should be carefully considered and justified to reduce LBA in phylogenetic reconstruction of different groups. Three subclades of J-C-HCX were estimated to have experienced ancient rapid divergence within a short period, which could be another major obstacle in resolving relationships. Furthermore, our plastid phylogenomic analyses fully resolved the intergeneric relationships of Cupressoideae.
类目[WOS]	Multidisciplinary Sciences
研究领域[WOS]	Science & Technology - Other Topics
关键词[WOS]	SPECIES TREE ESTIMATION ; SEED PLANT PHYLOGENY ; COMPOSITIONAL HETEROGENEITY ; PENALIZED LIKELIHOOD ; CHLOROPLAST GENOMES ; FLOWERING PLANTS ; ANIMAL PHYLOGENY ; SISTER GROUP ; EVOLUTION ; COALESCENT
收录类别	SCI
语种	英语
WOS记录号	WOS:000392660800001
内容类型	期刊论文
源URL	[http://ir.kib.ac.cn/handle/151853/45634]
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, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China 2.Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650201, Yunnan, Peoples R China 3.Acad Sinica, Biodivers Res Ctr, Taipei 11529, Taiwan
推荐引用方式 GB/T 7714	Qu, Xiao-Jian,Jin, Jian-Jun,Chaw, Shu-Miaw,et al. Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae)[J]. SCIENTIFIC REPORTS,2017,7.
APA	Qu, Xiao-Jian,Jin, Jian-Jun,Chaw, Shu-Miaw,Li, De-Zhu,&Yi, Ting-Shuang.(2017).Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae).SCIENTIFIC REPORTS,7.
MLA	Qu, Xiao-Jian,et al."Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae)".SCIENTIFIC REPORTS 7(2017).