The lycophyte genus Phlegmariurus (Herter) Holub (Huperzioideae, Lycopodiaceae) is ecologically and pharmaceutically significant, notably as a natural source of Huperzine A-a promising therapeutic candidate for Alzheimer's disease. Despite its medicinal potential, taxonomic ambiguities on species delimitation and infrageneric classification have impeded conservation and sustainable utilization efforts. Here, we assembled 40 Phlegmariurus complete chloroplast genomes, including all taxa from China, most of which were reported for the first time. Our results revealed the conserved quadripartite architectures and little variation in genome size and GC content in the genus. Comparative analyses on genome sequences identified seven hypervariable loci as prospective DNA barcodes for species discrimination. The phylogenetic toopologies reconstructed from nuclear ribosomal DNA and chloroplast genome data consistently resolved four monophyletic clades, further validated by SNP-based discriminant analysis of principal components. They are well corresponding to the four sections' classification on Chinese taxa (sect. Squarrosurus , sect. Phlegmariurus , sect. Fargesiani , sect. Hamiltoniani ). Notably, nuclear and chloroplast data congruently yielded a sister relationship between sect. Squarrosurus and sect. Phlegmariurus . However, the phylogenetic positions of sect. Fargesiani and sect. Hamiltoniani conflicted across different datasets. The diversification of the Chinese Phlegmariurus was traced back to the Oligocene (ca. 26.04 Ma). The comprehensive genetic resources generated herein provide a foundation for future research on species identification, population genomics and genetic diversity preservation in this medicinally significant vital genus.

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Understanding the diversity and ecological evolutionary history of plant species is crucial for addressing the current biodiversity crisis and comprehending the processes by which organisms fill ecological and geographic spaces. In this study, we present a comprehensive analysis of the diversity and evolutionary history of Diphasiastrum digitatum Holub from the lycophyte lineage of plants, using microsatellite genotyping data and biogeographic analyses. Based on the available transcriptome assembly, we generated numerous markers and utilized 13 robust microsatellite markers to genotype a collection of 402 specimens from the Eastern US (VT; VA; NC; TN). In accordance with the accepted phylogeny, cross-amplification tests demonstrated a closer relationship between D. digitatum and Diphasiastrum spp. compared with Lycopodium spp. Furthermore, the population genetics analyses identified two genetic clusters within the D. digitatum collection and suggested ongoing divergence and expansion. Isolation-by-distance analysis indicated that geographic distance had a minimal effect on differentiation, whereas environmental variables related to water regime were strongly associated with the genetic variance. Ecological niche modeling showed a post-Last Glacial Maximum expansion of D. digitatum from southern refugia, corroborating a similar evolutionary scenario based on our microsatellite data. Overall, this study provides valuable insights into the evolutionary history of clubmosses and highlights the migration events and the environmental factors that shaped their current distribution.

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The genus Phlegmariurus Holubis recognised more widely than originally proposed and is circumscribed to include both Neotropic and Palaeotropic epiphytic and terrestrial species of Huperzioid Lycopodiaceae that have isotomous shoots, lack bulbils in their sporophyllous shoots and have spores with convex lateral margins and foveolate-fossulate sculpture restricted to their distal surfaces. New combinations with Phlegmariurus are proposed for 81 species and existing combinations identified for 33 species originating from the Palaeotropics. This installs a generic circumscription that is consistent between the Neotropics and Palaeotropics. A lectotype is designated for the type species of the genus, Phlegmariurus phlegmaria (L.) T.Sen & U.Sen.

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A new alkaloid, phlegmariuine-N, was isolated from Phlegmariurus fordii (Baker) Ching. In the present work, a technique of long-range 1H-1H and 13C-1H COSY in combination with NOE difference spectroscopy has been successfully used to connect the spin systems separated by quatermary carbons and heteroatom. Its structure has been elucidated as (I).

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