Zhi-Qiong Mo

Summary: Accurate species identification is essential for biodiversity conservation and sustainable use, yet standard plant DNA barcoding often fails to achieve species‐level resolution. We present a large‐scale empirical evaluation of genome skimming as a tool to improve plant species discrimination. Using standardised data from 1969 individuals representing 475 species from 32 genera across major lineages of the vascular plant tree of life, we compare conventional plastid + internal transcribed spacer (ITS) barcodes with genome skimming approaches. Standard barcoding using rbcL , matK , trnH‐psbA and ITS resolved about half of species (49.3%), with six genera showing < 25% species discrimination. By contrast, genome skimming enabled the recovery of complete plastid genomes, yielding 57.6% species discrimination. It also generated sufficient nuclear genomic data for additional resolution from k‐mer analysis, achieving 66.8% species discrimination – an average gain of 17.5% over standard barcodes – while eliminating cases of extreme failure (< 25% resolution). The recovery of complete plastomes and ribosomal DNAs from genome skims also ensures backward compatibility with existing barcode datasets. Our results demonstrate that genome skimming provides data that substantially improves species‐level resolution across diverse plant lineages and offers a scalable, high‐throughput approach for building comprehensive reference resources to support global biodiversity initiatives.

Under anthropogenic global change, mountain plants are among the most threatened flora, making it essential to address conservation gaps to achieve the “30 × 30” target outlined in the Convention on Biological Diversity. Focusing on Rhododendron , the emblematic genus of montane ecosystems in Asia, we compiled an updated checklist of 603 Rhododendron species in China and integrated high‐resolution distribution, phylogenetic, functional trait, and environmental data to examine spatial diversity patterns, driving factors, and priority conservation areas. Our results indicated that the taxonomic, phylogenetic, and functional dimensions of Rhododendron diversity were highly consistent. The Three‐Parallel‐Rivers‐Region in the Hengduan Mountains emerged as the overarching hotspot for richness, endemism, and uniqueness. These diversity patterns were collectively influenced by temperature seasonality and elevation range, with temperature‐related energy factors further contributing to the overall phylogenetic and functional structures. The mechanisms underlying uniqueness exhibited regional divergence: In southwestern China, high uniqueness was attributed to the accumulation of intermediate‐aged and younger distinctive lineages, coupled with rapid community differentiation; in southern China, it was mainly associated with strong spatial compositional differentiation among communities; whereas in northeastern China, it largely resulted from the preservation of relict lineages. Under the 10% conservation target, we delineated nine priority conservation units across the southwestern, southern, and northeastern mountainous regions of China. However, when the conservation target was increased to 30%, these priority areas expanded to encompass broader mountain regions, highlighting a greater conservation gap. This study provides innovative insights for incorporating multidimensional diversity into effective conservation efforts for Rhododendron species in China.

The subfamily Monotropoideae (Ericaceae) comprises unique non-photosynthetic and mycoheterotrophic plants. Their extensive morphological reduction often poses significant challenges for species delimitation. In this study, we investigated an unknown Monotropa taxon collected from Hunan Province, China, through an integrative approach combining detailed morphological observation and phylogenetic analysis. We sequenced it, assembled the complete plastid genome and reconstructed phylogenetic trees using both chloroplast genomes and the nrITS region. Morphologically, this new entity is readily distinguished from its congener, Monotropa uniflora , by several key characteristics: 4–5 glabrous petals apically one-quarter orange and basally three-quarters white, 8–10 stamens with glabrous filaments, a nodding berry at maturity and a distinctly earlier flowering period (March–June vs. June–October). Phylogenetic reconstructions, based on both chloroplast genomes and nrITS data, consistently resolved this unknown taxon as a distinct lineage, clearly separating it from M. uniflora with strong support. Integrating evidence from morphology, phylogeny and phenology, we hereby describe it as a new species, Monotropa callistoma .

Premise: The placement of Sladeniaceae s.l. ( Sladenia and Ficalhoa ) within Ericales has remained contentious, largely due to incongruent molecular signals between plastid and nuclear loci and lack of clear morphological synapomorphies supporting its circumscription. Resolving its phylogenetic position is essential for clarifying evolutionary relationships along the backbone of Ericales. Methods: We used genome‐skimming and Angiosperms353 data to reconstruct plastid and nuclear phylogenies of Ericales, with comprehensive sampling of Sladeniaceae, Pentaphylacaceae, and allied families. Phytop and SNaQ analyses were applied to evaluate incomplete lineage sorting (ILS) and introgression. Divergence times were estimated using a relaxed‐clock birth–death model in the IQ2MC pipeline, and paleo‐niche modeling was used to infer the historical distribution of Sladenia . Results: Plastid phylogenies support the inclusion of Ficalhoa within Sladeniaceae, whereas nuclear trees place Ficalhoa as sister to Pentaphylacaceae, indicating strong cytonuclear discordance. Our analyses revealed a high level of incomplete lineage sorting at the nodes subtending Sladenia , Ficalhoa , and Pentaphylacaceae (ILS‐i = 84.8%), which may be explained by the rapid early diversification of core Ericales during the mid‐Cretaceous (~110–105 million years ago). No evidence of introgression was detected between Ficalhoa and Sladenia . Conclusions: Our findings suggest that stochastic sorting of ancestral plastid polymorphisms during rapid diversification may be the primary cause of cytonuclear discordance in the placement of Ficalhoa , although ancient plastid capture cannot be ruled out. These results support the inclusion of Ficalhoa within Pentaphylacaceae and underscore the roles of rapid diversification and incomplete lineage sorting in shaping deep phylogenetic relationships in Ericales.

Summary: Understanding how genomic architecture shapes patterns of gene flow is fundamental to unraveling the mechanisms of plant speciation. Here, we investigate whether differential gene flow dynamics between genomic spatial compartments play a role in speciation of Rhododendron subsect. Scabrifolia . We first present a chromosome‐level genome assembly for Rhododendron spinuliferum , and use this to characterize large‐scale chromatin organization, including A and B compartments. We then use genome resequencing data for 139 individuals from 15 populations of all eight species of R . subsect. Scabrifolia endemic to Southwest China to investigate speciation history. We find significant disparities in the extent of genomic differentiation between A and B compartments. The B compartment, closely associated with centromeres, tends to exhibit higher genetic differentiation, whereas the gene‐rich A compartment appears less differentiated and exhibits more extreme f _dm values, suggesting more extensive localized introgression. We propose that the heterogeneous nature of gene flow across genomic compartments contributes to speciation in Rhododendron , and may play a critical yet underappreciated role in gene flow dynamics in plants.

Over the past century, anthropogenic greenhouse gas emissions have continuously increased global temperature and triggered climate change, significantly impacting species distributions and biodiversity patterns. Understanding how climate-driven shifts in species distributions reshape diversity patterns is crucial for formulating effective future conservation strategies. Based on the distribution data of 314 Rhododendron species in China, along with 16 environmental variables, we examined spatial diversity patterns and assessed regional and biome differences in species responses using ensembled species distribution models. Our results indicated that climatic variables significantly influenced species distributions, with ongoing climate change expected to concentrate Rhododendron distribution patterns and alter species composition. Regional topography played a critical role in shaping species responses to global warming. In the mountainous areas of southwestern China, species exhibited heightened sensitivity to temperature fluctuations, shifting upward as temperature increased. This region also had a higher proportion of threatened species and showed an overall contraction in primary distribution range. Conversely, in southern China, species were more influenced by precipitation, exhibiting a notable northward shift and expansion in primary distribution areas. Notably, alpine species, occurring in habitats above the treeline, may face severe survival risks due to the high degree of habitat loss and fragmentation. We identified seven priority conservation areas, predominantly situated in highly fragmented mountainous regions that were inadequately protected by existing nature reserves. Our findings contribute to a better understanding of changes in Rhododendron diversity patterns under climate change, providing valuable insights for developing comprehensive, flora-wide conservation plans in China.

The study of natural hybridization facilitates our understanding of potential adaptive mechanisms in evolution and the process involved in speciation. In this study, we used multiple data types, including morphological traits, ddRAD-seq and ecological niche data, to investigate the differences among Rhododendron × duclouxii hybrid zones and the mechanisms underlying natural hybridization and possible future evolutionary pathways. Our results show that the origins of each hybrid zone are independent, with variations in hybrid formation, structural characteristics, and patterns of genetic components and morphological trait differentiation. There were no significant differences in morphological traits or genetic variation between the F₁ and F₂ generations; however, the range of variation of the F₂ generation was broader than that of the F₁ generation. The distribution and ecological characteristics of R. × duclouxii did not significantly differ from those of the two parental species, indicating weak ecological niche preferences between the hybrid and parental taxa. These results imply that the hybrid zones of R. × duclouxii are characterized by considerable variability, with the magnitude of hybridization in each case likely influenced by unique combinations of biological and ecological factors specific to each hybrid zone. We predict that R. × duclouxii hybrid zones will persist and give rise to complex hybrid swarms, each potentially leading to different evolutionary outcomes.

Summary: The structural and ecological significance of ericoid mycorrhizal (ErM) fungi is well recognized. Yet, it remains unknown whether the coexistence of ericaceous plants is facilitated by their symbioses with ErM fungi. Here, we use Rhododendron (Ericaceae) as a model to investigate how phylogenetic and functional limiting similarity, or facilitation through ErM fungal metacommunity, influences their co‐occurrence in mountain ecosystems. We found Rhododendron species tended to be phylogenetically and functionally clustered across elevations. However, a substantial dissimilarity in the composition of the putative ErM fungal community was observed among co‐occurring hosts within the same community, especially at higher elevations. Host identity played a predominant role in shaping the composition of the ErM fungal community. Moreover, the degree of network specialization in Rhododendron–ErM fungi interactions increased with elevation. Our study provides one of the first investigations into the drivers of ErM fungal community composition and network specialization in a species‐rich Rhododendron assemblage. Host‐symbiont mutualistic interactions in complex landscapes may offer insights into the coexistence of closely related species.

Magnolia buenaventurensis Á.J.Pérez & E.Rea 2023 is a newly described, endemic, and endangered species of the southwest Ecuadorian Andes mountains. Sequencing and characterizing its plastid genome will help clarify its relationship to other Neotropical Magnolia L. 1753. species. The plastid genome is 159,782 bp in length and includes 131 genes, 86 protein-coding genes (PCGs), 37 transfer RNAs (tRNA), and eight ribosomal RNA (rRNA) regions. Phylogenetic analysis confirms the species’ taxonomic classification in the section Talauma (Juss.) Baill 1866 and its close relationship to Magnolia gilbertoi (Lozano) Govaerts 1996 from Colombia, which belongs to the same section. However, the phylogenetic relationship shows low bootstrap support.

Deep genome skimming (DGS) has emerged as a promising approach to recover orthologous nuclear genes for large-scale phylogenomic analyses. However, its reliability with low DNA quality and quantity typical of archival specimens, such as herbarium material, remains largely unexplored. We used Rhododendron as a case study to evaluate best practices for DGS in phylogenetic analyses at both deep and shallow scales. We first investigated locus recovery variation with sequencing depth, before evaluating the phylogenetic utility of different sets of loci, including Angiosperms353, target nuclear exons, and extended exon-flanking regions. We found DGS effectively recovered nuclear genes from herbarium specimens, with ∼15× coverage performing similarly to deeper sequencing. The recovery of target exon and flanking regions was improved by using supercontigs as a reference, offering a potential solution to limited sequencing depth. The high-integrity nuclear sequences recovered robust phylogenetic relationships within Rhododendron. Notably, exon-flanking regions showed significant potential for resolving relationships at shallow scales. Genes recovered with taxon-specific references had less missing data than those recovered by Angiosperms353 and generated higher-resolution phylogenetic trees. This study demonstrates the utility of DGS data for obtaining numerous nuclear genes from herbarium specimens for phylogenetic studies, and makes recommendations for best practices regarding sequencing coverage, locus selection, and bioinformatic approaches.