Phylogeny of Diplazium (Athyriaceae) revisited: Resolving the backbone relationships based on plastid genomes and phylogenetic tree space analysis

doi:10.1016/j.ympev.2019.106699

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	Phylogeny of Diplazium (Athyriaceae) revisited: Resolving the backbone relationships based on plastid genomes and phylogenetic tree space analysis
	Wei, Ran ; Zhang, Xian-Chun
刊名	MOLECULAR PHYLOGENETICS AND EVOLUTION
	2020
卷号	143
关键词	Backbone Diplazium Evolutionary radiation Plastome Phylogenetic clustering
ISSN号	1055-7903
DOI	10.1016/j.ympev.2019.106699
文献子类	Article
英文摘要	Despite progress in resolving the phylogeny of twinsorus ferns (Diplazium) based on multilocus phylogenetic studies, uncertainty remains especially for deep, or backbone relationships among closely related clades, suggesting a classic case of rapid evolutionary radiation. Here, we investigated the deep phylogenetic relationships within Diplazium by sampling all major clades and using 51 plastid genomes (plastomes), of which 38 were newly sequenced with high-throughput sequencing technology, resulting more than 127,000 informative sites. Using parsimony, maximum likelihood and Bayesian analyses of plastome sequences, we largely resolved the backbone of the phylogeny of Diplazium with strong support. However, we also detected phylogenetic incongruence among different datasets and moderately to poorly supported relationships, particularly at several extremely short internal branches. By using phylogenetic tree space and topology-clustering analyses, we provide evidence that conflicting phylogenetic signals can be found across the trees estimated from individual chloroplast protein-coding genes, which may underlie the difficulty of systematics of Diplazium. Furthermore, our phylogenetic estimate offers more resolution over previous multilocus analyses, providing a framework for future taxonomic revisions of sectional classification of Diplazium. Our study demonstrates the advantage of a character-rich plastome dataset, combining the comparison of different phylogenetic methods, for resolving the recalcitrant lineages that have undergone rapid radiation and dramatic changes in evolutionary rates.
学科主题	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
电子版国际标准刊号	1095-9513
出版地	SAN DIEGO
WOS关键词	EUPOLYPOD II FERNS ; HORIZONTAL TRANSFER ; DEEP RELATIONSHIPS ; RAPID RADIATION ; DATA SET ; CHLOROPLAST ; EVOLUTION ; SUPPORT ; GENUS ; APPROXIMATION
WOS研究方向	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
语种	英语
出版者	ACADEMIC PRESS INC ELSEVIER SCIENCE
WOS记录号	WOS:000506225200026
资助机构	National Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31600175] ; External Cooperation Program of Bureau of International Co-operation Chinese Academy of Sciences [GJHZ201321]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/21953]
专题	系统与进化植物学国家重点实验室
作者单位	1.[Wei, Ran 2.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Wei, Ran,Zhang, Xian-Chun. Phylogeny of Diplazium (Athyriaceae) revisited: Resolving the backbone relationships based on plastid genomes and phylogenetic tree space analysis[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2020,143.
APA	Wei, Ran,&Zhang, Xian-Chun.(2020).Phylogeny of Diplazium (Athyriaceae) revisited: Resolving the backbone relationships based on plastid genomes and phylogenetic tree space analysis.MOLECULAR PHYLOGENETICS AND EVOLUTION,143.
MLA	Wei, Ran,et al."Phylogeny of Diplazium (Athyriaceae) revisited: Resolving the backbone relationships based on plastid genomes and phylogenetic tree space analysis".MOLECULAR PHYLOGENETICS AND EVOLUTION 143(2020).