Plant Diversity ›› 2024, Vol. 46 ›› Issue (02): 194-205.DOI: 10.1016/j.pld.2023.10.004

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Cryptic diversity and rampant hybridization in annual gentians on the Qinghai-Tibet Plateau revealed by population genomic analysis

Peng-Cheng Fua, Qiao-Qiao Guoa, Di Changa, Qing-Bo Gaob, Shan-Shan Suna   

  1. a. School of Life Science, Luoyang Normal University, Luoyang 471934, PR China;
    b. Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, PR China
  • Received:2023-04-26 Revised:2023-10-24 Online:2024-03-25 Published:2024-04-07
  • Contact: Peng-Cheng Fu,
  • Supported by:
    We are grateful to financial support provided by the Foundation of Henan Educational Committee (22A180024) and Natural Science Foundation of Henan Province (232300420212).

Abstract: Understanding the evolutionary and ecological processes involved in population differentiation and speciation provides critical insights into biodiversity formation. In this study, we employed 29,865 single nucleotide polymorphisms (SNPs) and complete plastomes to examine genomic divergence and hybridization in Gentiana aristata, which is endemic to the Qinghai-Tibet Plateau (QTP) region. Genetic clustering revealed that G. aristata is characterized by geographic genetic structures with five clusters (West, East, Central, South and North). The West cluster has a specific morphological character (i.e., blue corolla) and higher values of FST compared to the remaining clusters, likely the result of the geological barrier formed by the Yangtze River. The West cluster diverged from the other clusters in the Early Pliocene; these remaining clusters diverged from one another in the Early Quaternary. Phylogenetic reconstructions based on SNPs and plastid data revealed substantial cyto-nuclear conflicts. Genetic clustering and D-statistics demonstrated rampant hybridization between the Central and North clusters, along the Bayankala Mountains, which form the geological barrier between the Central and North clusters. Species distribution modeling demonstrated the range of G. aristata expanded since the Last Interglacial period. Our findings provide genetic and morphological evidence of cryptic diversity in G. aristata, and identified rampant hybridization between genetic clusters along a geological barrier. These findings suggest that geological barriers and climatic fluctuations have an important role in triggering diversification as well as hybridization, indicating that cryptic diversity and hybridization are essential factors in biodiversity formation within the QTP region.

Key words: Gentiana aristata, Hybrid zone, Qinghai-Tibet Plateau, Plastome, Nuclear SNPs