Niche transition and trait differentiation in Chinese Huperzia : a “museum–cradle” perspective

Understanding how species diversity originates, accumulates and is sustained across heterogeneous regions is a core goal of macroevolutionary and conservation biology. The genus Huperzia is an ancient and cosmopolitan lineage of lycophytes, with species widely distributed in both temperate alpine and subtropical low- to mid-elevation areas, offering ideal material for investigating the diversification history of early vascular plant lineages. Here, we utilized 87 plastid genomes from 23 species to reconstruct a robust phylogenetic framework within Huperzia and found that the development of the petiole and midrib should be considered supplementary diagnostic characters in future taxonomic revisions. Our spatiotemporal and spatial phylogenetic analyses indicated that temperate and montane regions, especially northeastern China and parts of the Qinghai-Tibet Plateau, preserve phylogenetically distinctive paleo-lineages, whereas subtropical evergreen broad-leaved forests contain younger lineages associated with ecological expansion and trait differentiation. This niche transition was accompanied by repeated leaf-trait differentiation and shifts in plastid-gene selection in subtropical lineages, with three positively selected genes (rps19, chlB and atpH) identified by branch-site analyses. This evolutionary strategy provides a new perspective for understanding how early vascular plants maintained a dynamic equilibrium between refugial conservatism and adaptive innovation.