Journal of Systematics and Evolution

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  • 收稿日期:2020-01-16 接受日期:2020-05-01

Genomic data reveal two distinct species from the widespread alpine ginger Roscoea tibetica Batalin (Zingiberaceae)

Li Li1,2, Jie Zhang3,4, Zhi-Qiang Lu1,2, Jian-Li Zhao3,4*, and Qing-Jun Li3,4*   

  1. 1CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla666303, Yunnan, China
    2University of Chinese Academy of Sciences, Beijing 100049, China
    3Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, Yunnan University, Kunming 650500, China
    4Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming 650500, China
  • Received:2020-01-16 Accepted:2020-05-01


Species delimitation is a key foundation for exploring biodiversity. However, the existence of continuous phenotypic variation in widespread species challenges accurate species delimitation based on classical taxonomy. In this study, we investigated the cryptic diversity of a widespread herb (Roscoea tibetica Batalin) in a biodiversity hotspot (the Hengduan Mountains, China) using genotyping by sequencing, examining morphological traits, developing species distribution models, and simulating demographic history. Phylogenomic reconstruction, principal component analysis, and genetic structure inferences indicated that previously reported R. tibetica comprised two monophyletic lineages with a deep divergence. Several morphological diagnostic characteristics were discovered from field and common garden that corresponded to these independent evolutionary lineages. Species distribution models illustrated significant ecological divergence between both lineages. All evidence strongly supported that R. tibetica , as described in previous taxonomy, actually comprises two distinct species. Model test of gene flow and effective population size changes in fastsimcoal2, and a negative Tajima's D ‐value suggested that recent contact likely occurred between the two lineages. Our results proposed that cryptic diversity in previously reported R. tibetica was possibly associated with phenotypic plasticity in heterogeneous environments and morphological convergence in similar habitats. This study suggests that caution should be exercised when attempting to gain biological insight into species with large‐scale morphological variation, and species delimitation should be done in advance.

Key words: cryptic species, genotyping by sequencing, phylogenomics, Roscoea tibetica, species delimitation