Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity

doi:10.1007/s11104-017-3400-0

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	Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity
	Wei, Ran ; Yan, Yue-Hong ; Harris, A. J.; Kang, Jong-Soo ; Shen, Hui 5; Xiang, Qiao-Ping ; Zhang, Xian-Chun
刊名	GENOME BIOLOGY AND EVOLUTION
	2017
卷号	9 期号:6 页码:1646-1657
关键词	Aspleniaceae Athyriaceae backbone phylogeny plastome substitution rate Rhachidosoraceae
ISSN号	1759-6653
DOI	10.1007/s11104-017-3400-0
文献子类	Article
英文摘要	The eupolypods II ferns represent a classic case of evolutionary radiation and, simultaneously, exhibit high substitution rate heterogeneity. These factors have been proposed to contribute to the contentious resolutions among clades within this fern group in multilocus phylogenetic studies. We investigated the deep phylogenetic relationships of eupolypod II ferns by sampling all major families and using 40 plastid genomes, or plastomes, of which 33 were newly sequenced with next-generation sequencing technology. We performed model-based analyses to evaluate the diversity of molecular evolutionary rates for these ferns. Our plastome data, with more than 26,000 informative characters, yielded good resolution for deep relationships within eupolypods II and unambiguously clarified the position of Rhachidosoraceae and the monophyly of Athyriaceae. Results of rate heterogeneity analysis revealed approximately 33 significant rate shifts in eupolypod II ferns, with the most heterogeneous rates (both accelerations and decelerations) occurring in two phylogenetically difficult lineages, that is, the Rhachidosoraceae-Aspleniaceae and Athyriaceae clades. These observations support the hypothesis that rate heterogeneity has previously constrained the deep phylogenetic resolution in eupolypods II. According to the plastome data, we propose that 14 chloroplast markers are particularly phylogenetically informative for eupolypods II both at the familial and generic levels. Our study demonstrates the power of a character-rich plastome data set and high-throughput sequencing for resolving the recalcitrant lineages, which have undergone rapid evolutionary radiation and dramatic changes in substitution rates.
学科主题	Agriculture ; Plant Sciences
出版地	OXFORD
WOS关键词	CHLOROPLAST PHYLOGENOMICS ; PHYLOGENETIC ANALYSES ; SEQUENCE ; CLASSIFICATION ; SOFTWARE ; GENOME ; FAMILY ; TIME ; POLYPODIIDAE ; ATHYRIACEAE
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000417721600036
资助机构	National Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31600175, 31470317] ; External Cooperation Program of Bureau of International Co-operation Chinese Academy of Sciences [GJHZ201321] ; Shanghai Municipal Administration of Forestation and City Appearances Grant [G152420]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/22047]
专题	系统与进化植物学国家重点实验室
作者单位	1.Kang, Jong-Soo 2.[Wei, Ran 3.Xiang, Qiao-Ping 4.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 5.[Yan, Yue-Hong 6.Chinese Acad Sci, Shanghai Chenshan Plant Sci Res Ctr, Shanghai Chenshan Bot Garden, Shanghai Key Lab Plant Funct Genom & Resources, Shanghai, Peoples R China 7.[Harris, A. J.] Smithsonian Inst, Dept Bot, Natl Museum Nat Hist, Washington, DC 20560 USA 8.Univ Chinese Acad Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Wei, Ran,Yan, Yue-Hong,Harris, A. J.,et al. Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity[J]. GENOME BIOLOGY AND EVOLUTION,2017,9(6):1646-1657.
APA	Wei, Ran.,Yan, Yue-Hong.,Harris, A. J..,Kang, Jong-Soo.,Shen, Hui.,...&Zhang, Xian-Chun.(2017).Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity.GENOME BIOLOGY AND EVOLUTION,9(6),1646-1657.
MLA	Wei, Ran,et al."Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity".GENOME BIOLOGY AND EVOLUTION 9.6(2017):1646-1657.