Plastome-based phylogeny improves community phylogenetics of subtropical forests in China

doi:10.1111/1755-0998.13462

	Plastome-based phylogeny improves community phylogenetics of subtropical forests in China
	Jin, Lu ; Liu, Jia-Jia ; Xiao, Tian-Wen ; Li, Qiao-Ming ; Lin, Li-Xiang ; Shao, Xiao-Na ; Ma, Chen-Xin ; Li, Bu-Hang ; Mi, Xiang-Cheng ; Ren, Hai-Bao ; Qiao, Xiu-Juan ; Lian, Ju-Yu ; Hao, Gang ; Ge, Xue-Jun
	2022
发表期刊	MOLECULAR ECOLOGY RESOURCES
ISSN	1755-098X
卷号	22 期号:1 页码:319-333
摘要	Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.
关键词	alpha diversity community phylogeny DNA barcoding phylogenetic community structure phylogenetic phylogenetic beta diversity phylogenetic signal plastid genome
学科领域	Biochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
DOI	10.1111/1755-0998.13462
收录类别	SCI
语种	英语
WOS关键词	NICHE CONSERVATISM ; R PACKAGE ; EVOLUTIONARY ; DIVERSITY ; PATTERNS ; SEQUENCE ; ECOLOGY ; ANGIOSPERMS ; ANNOTATION ; SOFTWARE
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000673747200001
出版者	WILEY
文献子类	Article
出版地	HOBOKEN
EISSN	1755-0998
资助机构	National Natural Science Foundation of China [31500335] ; Strategic Priority Research Program of the Chinese Academy of Sciences [XDB31000000]
作者邮箱	haogang@scau.edu.cn ; xjge@scbg.ac.cn
引用统计	被引频次：8[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/28589
专题	植被与环境变化国家重点实验室
作者单位	1.South China Agr Univ, Coll Life Sci, Guangzhou, Peoples R China 2.Chinese Acad Sci, Key Lab Plant Resources Conservat & Sustainable U, South China Bot Garden, Guangzhou, Peoples R China 3.Chinese Acad Sci, CAS Key Lab Trop Forest Ecol, Xishuangbanna Trop Bot Garden, Kunming, Yunnan, Peoples R China 4.Univ Chinese Acad Sci, Beijing, Peoples R China 5.Sun Yat Sen Univ, Sch Life Sci, Guangzhou, Peoples R China 6.Chinese Acad Sci, Inst Bot, State Key Lab Vegetat & Environm Change, Beijing, Peoples R China 7.Chinese Acad Sci, Key Lab Aquat Bot & Watershed Ecol, Wuhan Bot Garden, Wuhan, Peoples R China 8.Chinese Acad Sci, Ctr Conservat Biol, Core Bot Gardens, Wuhan, Peoples R China 9.Chinese Acad Sci, Ctr Plant Ecol, Core Bot Gardens, Guangzhou, Peoples R China
推荐引用方式 GB/T 7714	Jin, Lu,Liu, Jia-Jia,Xiao, Tian-Wen,et al. Plastome-based phylogeny improves community phylogenetics of subtropical forests in China[J]. MOLECULAR ECOLOGY RESOURCES,2022,22(1):319-333.
APA	Jin, Lu.,Liu, Jia-Jia.,Xiao, Tian-Wen.,Li, Qiao-Ming.,Lin, Li-Xiang.,...&Ge, Xue-Jun.(2022).Plastome-based phylogeny improves community phylogenetics of subtropical forests in China.MOLECULAR ECOLOGY RESOURCES,22(1),319-333.
MLA	Jin, Lu,et al."Plastome-based phylogeny improves community phylogenetics of subtropical forests in China".MOLECULAR ECOLOGY RESOURCES 22.1(2022):319-333.

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