Yue-Hua Wang

Genetic exchanges underpin population adaptation and species evolution. However, knowledge of the genetic impacts of historical, anthropogenic crop-to-wild gene flow remains limited. In southwestern China, the long cultivation and parapatric distribution of Juglans regia and J. sigillata provide an ideal system to investigate this process, yet the evolutionary origin of the cultivated walnut in this region remains a mystery. Using 31 microsatellite loci to genotype 2,866 individuals, along with 716 chloroplast genomes, we evaluated genetic diversity, population structure, and maternal lineage patterns across the region. Population demographic histories were subsequently inferred using approximate Bayesian computation. Our analysis revealed that J. sigillata has higher genetic diversity than J. regia, attributed to its long-term persistence in heterogeneous environments. We observed extensive hybridization between the two species around the Sichuan Basin, forming two geographically distinct subgroups: Hybrid1 in the northwest and Hybrid2 in the south. Both subgroups exhibit variable parental contributions, but with the chloroplast genome entirely introgressed from J. regia. Furthermore, the Sichuan Basin and Yangtze River acted as major geographic barriers to north-south gene flow. Our divergence time estimates showed that the two species diverged during the Pleistocene, followed by an admixture event between J. regia and J. sigillata, forming Hybrid2 during the early Holocene. Subsequent admixture between Hybrid2 and J. regia produced Hybrid1 during the middle Holocene. We propose that cultivated walnuts in southwestern China originated through introgression between J. regia and wild J. sigillata during the Holocene, prior to the introduction of agriculture to the region, a process likely facilitated by historical southward human migrations. This research elucidates how long-term human influence has subtly reshaped the genetic landscape of walnuts in southwestern China through gene flow, providing valuable insights for the study and management of other tree crops.

The evolutionary history of Yunnanopilia longistaminea, a vulnerable plant endemic to the Yuanjiang-Honghe River Valley in southwestern China, was investigated using cpDNA and nrDNA sequences along with ecological niche modeling. Understanding the genetic diversity and population structure of Y. longistaminea is crucial for developing effective conservation strategies and managing its genetic resources. This study comprehensively sampled 295 individuals from 16 populations, which represent the species’ entire global distribution range, ensuring a thorough and representative analysis of its genetic diversity and population structure. The results revealed high genetic diversity and population structure, with significant genetic differentiation among populations. Specifically, the total nucleotide diversity was 2.40 × 10⁻³ for cpDNA and 1.51 × 10⁻³ for nrDNA, while the total haplotype diversity was 0.605 for cpDNA and 0.526 for nrDNA. The divergence time of ancestral haplotypes of Y. longistaminea was estimated to be around 2.19 million years ago based on nrDNA and 2.72 million years ago based on cpDNA. These divergence times are comparable to those of other ancient plant species, suggesting a long evolutionary history. The population size of Y. longistaminea was found to have significantly declined around 30,000 years ago. The current distribution model suggests that Y. longistaminea primarily inhabits the warm temperate zone of China, and the LGM distribution model predicts a concentration of the species in Yuanjiang-Honghe River Valley in southwestern China. This study concludes that the southwestern region of China may have served as a glacial refuge for Y. longistaminea. These findings suggest that establishing protected areas in these regions and creating gene banks for ex situ conservation could be effective strategies to preserve the genetic diversity of Y. longistaminea. Further research on its population dynamics and genetic adaptation to climate change is valuable for understanding the species’ evolutionary history and conservation.

The mulberry genus, Morus L. (Moraceae), has long been taxonomically difficult, and its species circumscription has only been defined recently. This genus comprises ca. 16 species distributed across Asia and the Americas, yet its biogeographic history remains poorly understood. In this study, we reconstructed the phylogeny and explored the biogeographic history of Morus using a combination of newly generated and previously published Hyb-Seq data. Our nuclear phylogeny recovered three well-supported geographic clades of Morus and showed that M. notabilis (China) is sister to the American clade plus the Asian clade. Multiple reticulation events among species of Morus and extensive incomplete lineage sorting (ILS) likely explain the difficulties in inferring phylogenetic relationships within the genus. Divergence time estimation indicated that Morus originated at the Eocene–Oligocene boundary, and current lineages started to diverge during the early Miocene, there is ambiguity surrounding the ancestral area with the two most likely regions being Sino-Himalaya or the Americas. Biogeographic inference and the fossil record suggest that Morus might have experienced extensive local extinction events during the Tertiary. Morus has expanded its distributional range through two dispersals from the Sino-Himalayan and Sino-Japanese regions to Southeast Asia. In summary, our new phylogenetic scheme and the biogeographic history presented here provide an essential foundation for understanding species relationships and the evolutionary history of Morus.

Silene ophioglossa Huan C. Wang & Feng Yang, a new species of Caryophyllaceae, is here described and illustrated based on morphological and molecular evidence. The new species was found in Sichuan and Yunnan provinces, southwest China. Phylogenetic analysis based on ITS sequences showed this new species belongs to section Cucubaloides. Morphologically, it resembles S. phoenicodonta and S. viscidula, which were also found in the southwest China, but clearly differs from the latter two species by having 5–7 mm long calyces with sparsely hirtellous and short glandular hairs, white petals, linear limbs and lobes, and absent or oblong-linear coronal scales. A distribution map and a table with morphological diagnostic characters of new species and its closest relatives are provided, as well as a preliminary conservation assessment of S. ophioglossa under the IUCN criteria.

A lakeside is a functional transition zone that connects the lake aquatic ecosystem and the land ecosystem. Understanding the community assembly mechanism is crucial for regional ecological restoration, habitat management, and biodiversity conservation. However, research on the terrestrial plant community assembly in lakesides under anthropogenic disturbance is still lacking. The present study used phylogeny and functional traits to assess the community assembly of three habitat types with different anthropogenic disturbances in Dianchi lakeside. The factors that influenced the community assembly were also explored. Results indicated that the phylogenetic signals of all the examined functional traits of the dominant species were weak, suggesting that the traits were convergent. The community phylogenetic and functional structures of the different habitat types showed random patterns. Thus, the assembly of terrestrial plant communities in the three habitat types was driven by competitive exclusion and neutral processes in Dianchi lakeside. The trait trade-off strategies of species in the different habitats varied with the different habitat types. Anthropogenic disturbance played an important role in the process of community assembly. The present study provides a scientific basis for the assessment and management of ecological restoration in Dianchi lakeside and other plateau lakes and enriches the knowledge on the community assembly mechanism of disturbed plant communities.

In this study, we determined the complete chloroplast genome of Cycas hongheensis (Cycadaceae), one of the first-class protected plants in China. The chloroplast genome is 162,048 bp in length with 133 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content is 39.4%. Phylogenomic analysis showed that C. hongheensis as sister to all other Cycas species that with reported chloroplast genomes. The chloroplast genome of C. hongheensis reported here will contribute to further comparative chloroplast genome of Cycads and helpful to study the phylogeography of Cycadaceae.

To clarify the taxonomic status of Arundinella setosa var. tengchongensis and its relationships with A. setosa var. setosa and other related species, molecular phylogenetic analyses based on nuclear ITS and two plastid DNA ( matK and trnL‐F ) sequences, and morphological comparisons using one‐way ANOVA were carried out. Our results reveal that A. setosa var. tengchongensis phylogenetically belong in a different clade separated from the type variety. Morphologically, A. setosa var. tengchongensis is easily distinguished from A. setosa var. setosa and other varieties by its smaller spikelets, shorter awns and bearded nodes. Thus, A. setosa var. tengchongensis is here elevated to species rank and newly combined as A. tengchongensis .

Trachycarpus nanus is an endangered plant that is endemic to southwest of China. In the present study, the complete chloroplast genome of this species was assembled and characterized using whole genome next-generation sequencing. The complete chloroplast genome showed a circular genome of 158,713 bp size with 36.6% GC content. The genome is of typical structure and contain a pair of inverted repeat (IR) regions with 27,240 bp, separated by one large single-copy (LSC) with 86,395 bp, and one small single-copy (SSC) regions with 17,838 bp. The genome contained 132 genes, including 86 protein-coding genes, 8 rRNA genes and 38 tRNA genes. A phylogenetic tree reconstructed based on 21 chloroplast genomes reveals that Trachycarpus nanus is most related with Chamaerops humilis. The information provides important genetic basis for the species’ future studies on phylogenetic and utilization.

Impatiens wutaishanensis R.L. Liao & Lei Cai, a new species from Southeast Yunnan, China, is here described and illustrated. This new species is most similar to Impatiens parvisepala S.X. Yu & Y.T. Hou in its racemose inflorescences, its four lateral sepals, the leaf arrangement, and in having yellow flowers. However, it differs in the height of the plants, the length of the petiole, the size and shape of the leaf blade, the shape of the spur, and the number of flowers in each inflorescence. A detailed description, color photographs, and a provisional IUCN red list assessment are provided, and its geographical distribution, ecology, and morphological relationship with relevant similar species are discussed.

Natural hybridization is frequent in plants and is considered an important factor facilitating speciation. The natural intergeneric hybridization between Ligularia and Cremanthodium was previously confirmed using a couple of DNA markers. However, the mechanism of this intergeneric hybridization and the role of reproductive isolation in the process of hybridization remain unclear. Here we used double-digest restriction site-associated DNA sequencing (ddRAD-seq) to further quantify the occurrence of hybridization, the genetic structure of the hybrid population and the role of reproductive isolation between Ligularia nelumbifolia and Cremanthodium stenoglossum. The results based on the ddRAD-seq SNP data sets indicated that hybridization between L. nelumbifolia and C. stenoglossum was restricted to F₁s, and no gene introgression was identified between these two species. STRUCTURE analysis and maximum likelihood (ML) tree results showed a slightly larger genetic contribution of L. nelumbifolia to putative hybrid F₁s. We deduced that the reproductive isolation between these two parent species is not well-developed but still strong enough to maintain the genetic integrity of the species, and that their F₁s are sterile or with low fertility. Given the poorly resolved phylogenetic relationship between Ligularia and Cremanthodium, the occurrence of natural hybridization between L. nelumbifolia and C. stenoglossum may provide new insights into the re-circumscription and re-delimitation of these two genera.