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Molecular phylogeny and species delimitation of Stachyuraceae: Advocating a herbarium specimen-based phylogenomic approach in resolving species boundaries
Su, Jun-Xia; Dong, Cong-Cong; Niu, Yan-Ting; Lu, Li-Min; Xu, Chao; Liu, Bing; Zhou, Shi-Liang; Lu, An-Ming; Zhu, Yu-Ping; Wen, Jun4; Chen, Zhi-Duan
2020
Source PublicationJOURNAL OF SYSTEMATICS AND EVOLUTION
ISSN1674-4918
Volume58Issue:5Pages:710-724
AbstractSpecies concept and delimitation are fundamental to taxonomic and evolutionary studies. Both inadequate informative sites in the molecular data and limited taxon sampling have often led to poor phylogenetic resolution and incorrect species delineation. Recently, the whole chloroplast genome sequences from extensive herbarium specimen samples have been shown to be effective to amend the problem. Stachyuraceae are a small family consisting of only one genusStachyurusof six to 16 species. However, species delimitation inStachyurushas been highly controversial because of few and generally unstable morphological characters used for classification. In this study, we sampled 69 individuals of seven species (each with at least three individuals) covering the entire taxonomic diversity, geographic range, and morphological variation ofStachyurusfrom herbarium specimens for genome-wide plastid gene sequencing to address species delineation in the genus. We obtained high-quality DNAs from specimens using a recently developed DNA reconstruction technique. We first assembled four whole chloroplast genome sequences. Based on the chloroplast genome and one nuclear ribosomal DNA sequence ofStachyurus, we designed primers for multiplex polymerase chain reaction and high throughput sequencing of 44 plastid loci for species ofStachyurus. Data of these chloroplast DNA and nuclear ribosomal DNA internal transcribed spacer sequences were used for phylogenetic analyses. The phylogenetic results showed that the Japanese speciesStachyurus praecoxSiebold & Zucc. was sister to the rest in mainland China, which indicated a typical Sino-Japanese distribution pattern. Based on diagnostic morphological characters, distinct distributional range, and monophyly of each clade, we redefined seven species forStachyurusfollowing an integrative species concept, and revised the taxonomy of the family based on previous reports and specimens, in particular the type specimens. Furthermore, our divergence time estimation results suggested that Stachyuraceae split from its sister group Crossosomataceae from the New World at ca. 54.29 Mya, but extant species of Stachyuraceae started their diversification only recently at ca. 6.85 Mya. Diversification time ofStachyurusin mainland China was estimated to be ca. 4.45 Mya. This research has provided an example of using the herbarium specimen-based phylogenomic approach in resolving species boundaries in a taxonomically difficult genus.
Keywordchloroplast genome DNA reconstruction phylogeny specimen-based taxon sampling Stachyuraceae
Subject AreaPlant Sciences
DOI10.1111/jse.12650
Indexed BySCI
Language英语
WOS KeywordCHLOROPLAST GENOME ; GENETIC-DIVERGENCE ; SOFTWARE ; DNA ; DISJUNCTIONS ; SEQUENCES ; RISE ; ASIA
WOS Research AreaPlant Sciences
WOS IDWOS:000552397600001
PublisherWILEY
Special IssueSI
SubtypeArticle
Publication PlaceHOBOKEN
EISSN1759-6831
Funding OrganizationStrategic Priority Research Program of CAS [XDB31000000, XDA19050103] ; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31590822, 31300180] ; Sino-Africa Joint Research Center, Chinese Academy of Sciences, CAS International Research and Education Development Program [SAJC201613]
Corresponding Author Emailwenj@si.edu ; zhiduan@ibcas.ac.cn
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Cited Times:5[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ibcas.ac.cn/handle/2S10CLM1/21659
Collection系统与进化植物学国家重点实验室
Affiliation1.Shanxi Normal Univ, Coll Life Sci, Linfen 041000, Shanxi, Peoples R China
2.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China
3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
4.Nanjing Univ, Sch Life Sci, Nanjing 210023, Peoples R China
5.Smithsonian Inst, Dept Bot, Natl Museum Nat Hist, Washington, DC 20013 USA
Recommended Citation
GB/T 7714
Su, Jun-Xia,Dong, Cong-Cong,Niu, Yan-Ting,et al. Molecular phylogeny and species delimitation of Stachyuraceae: Advocating a herbarium specimen-based phylogenomic approach in resolving species boundaries[J]. JOURNAL OF SYSTEMATICS AND EVOLUTION,2020,58(5):710-724.
APA Su, Jun-Xia.,Dong, Cong-Cong.,Niu, Yan-Ting.,Lu, Li-Min.,Xu, Chao.,...&Chen, Zhi-Duan.(2020).Molecular phylogeny and species delimitation of Stachyuraceae: Advocating a herbarium specimen-based phylogenomic approach in resolving species boundaries.JOURNAL OF SYSTEMATICS AND EVOLUTION,58(5),710-724.
MLA Su, Jun-Xia,et al."Molecular phylogeny and species delimitation of Stachyuraceae: Advocating a herbarium specimen-based phylogenomic approach in resolving species boundaries".JOURNAL OF SYSTEMATICS AND EVOLUTION 58.5(2020):710-724.
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