J Syst Evol ›› 2020, Vol. 58 ›› Issue (5): 710-724.DOI: 10.1111/jse.12650

• Research Articles • Previous Articles     Next Articles

Molecular phylogeny and species delimitation of Stachyuraceae: Advocating a herbarium specimen‐based phylogenomic approach in resolving species boundaries

Jun-Xia Su1† , Cong-Cong Dong1† , Yan-Ting Niu2,3, Li-Min Lu2 , Chao Xu2 , Bing Liu2 , Shi-Liang Zhou2 , An-Ming Lu2 , Yu-Ping Zhu4 , Jun Wen5*, and Zhi-Duan Chen2*   

  1. 1 College of Life Sciences, Shanxi Normal University, Linfen 041000, China
    2 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
    3 University of Chinese Academy of Sciences, Beijing 100049, China
    4 School of Life Sciences, Nanjing University, Nanjing 210023, China
    5 Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013‐7012, USA
  • Received:2019-03-12 Accepted:2020-05-09 Online:2020-06-24 Published:2020-09-01


Species 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 genus Stachyurus of six to 16 species. However, species delimitation in Stachyurus has 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 of Stachyurus from 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 of Stachyurus, we designed primers for multiplex polymerase chain reaction and high throughput sequencing of 44 plastid loci for species of Stachyurus. 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 species Stachyurus praecox Siebold & 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 for Stachyurus following 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 of Stachyurus in 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.

Key words: chloroplast genome, DNA reconstruction, phylogeny, specimen-based taxon sampling, Stachyuraceae