Polyploidy is an important evolutionary force increasing plant diversity and environmental resilience. Reconstructing genome size (GS) and ploidy of plant fossils advances our understanding of plant evolution and stress adaptation. Palaeopolyploidy is usually inferred from molecular data, but precise timing of polyploidy events requires improvement. So far there has been no robust fossil evidence for palaeopolyploidy in angiosperms. Here, the GS of late Eocene (similar to 34.6 Ma, the Markam flora) and Middle Miocene (similar to 15 Ma, the Namling flora) sclerophyllous oak (Quercus sect. Heterobalanus) fossils from southern Tibet, and three Late Pliocene fossils from Yunnan, China, were derived using the strong positive correlation between guard cell length (GCL) and GS. The estimated GS of the Namling fossils was approximately double those of late Eocene and Late Pliocene fossils as well as extant samples, indicating that the Namling fossils probably experienced a polyploidisation event. These tetraploids seemingly conferred greater resilience to aridity and cold-induced stress after similar to 15 Ma, reflected by two distinct fossil assemblages preserved in this flora, coincident with uplift of the Gangdese. Our discovery of sclerophyllous oak tetraploids provides compelling fossil evidence for palaeopolyploids in angiosperms, and demonstrates plant adaptation at the genome level to regional climatic change triggered by mountain uplift. GCL analysis serves as a promising tool for investigating GS changes across land plant evolution. Future research of elucidating the drivers of GCL variation is essential for enhancing the precision and reliability of this proxy.

Land plants underpin civilization and planetary health, yet their genomic diversity remains largely uncharted. Current resources are unstandardized and scarce, lacking reference genomes for 95% of genera, 70% of families, and 51% of orders, impeding evolutionary and functional insight. We thus propose the PLANeT initiative, an international effort to generate high-quality, standardized genomes across the plant tree of life. Integrating artificial intelligence (AI) with genomics, we will decode conserved principles to advance fundamental plant biology, biodiversity conservation, crop improvement, and natural product discovery. Engaging around 100 labs to train 1,000 scientists, we will tackle pivotal questions for a sustainable future.

Abundant and exceptionally well-preserved Tilia macrofossils from Early and Middle Miocene deposits in Korea provide a rare multi-organ fossil record, including flowers, fruits (nutlets), bracts, and leaves. Notably, the material represents one of the most complete fossil flowers yet reported for Tilia, preserved with a beaker-shaped perianth and diagnostic internal lamellae, enabling confident floral-androecial interpretation. Systematic study documents two new species-T. pentagona sp. nov., characterized by a Type C leaf-like bract and a ribbed, mamillate nutlet with a pentagonal cross-section, and T. perpendicularis sp. nov., based on the well-preserved flower-and further assigns additional organs to T. tomentosella, T. asiatica, and T. miohenryana. In contrast to the two native species (T. amurensis and T. mandshurica) present in Korea today, our findings demonstrate that Miocene Korea supported a richer Tilia assemblage than today. A biogeographical synthesis, informed by the stratigraphic distribution of Tilia fossils and deep-time ecological niche modeling, indicates that suitable habitats encompassed Korea during the Miocene but contracted markedly thereafter, consistent with the Quaternary cooling. Together, our findings enrich the fossil record of Tilia and reveal that the favorable Miocene climates in Korea fostered a higher diversity of the genus.

Mountain regions harbor extraordinary biodiversity, yet the mechanisms underlying this pattern remain unclear. Here we use the phylogenetically and geographically replicated radiations of Berberis (barberries) in the Andes and Hengduan-Himalaya Mountains (HHM) to test how functional trait innovations, orogeny, and climate change influenced the buildup of species richness in each region. In barberries (Berberis), the successive evolution of deciduousness and small, densely-veined leaves enabled the lineage to take advantage of expanding alpine and subalpine habitats in the HHM during the Miocene. The resulting pulse in the origin of new species contrasts with the more modest rate of species accumulation in the Andes, where barberry species remained evergreen and the availability of high-elevation habitats was more limited. In this study, the phylogeny of barberries exemplifies context-dependent macroevolutionary dynamics, in which intrinsic innovations and extrinsic ecological opportunities interacted to generate exceptional plant diversity in a mountain hotspot.

Abstract Mountain regions of the Northern Hemisphere harbor exceptional biodiversity, yet the processes underlying species diversification and migration among these regions remain poorly understood. This study investigates the macroevolutionary dynamics of Androsace s.l ., a genus widely distributed across temperate regions of the Northern Hemisphere, with notable diversity in the Alps and the Hengduan–Himalaya regions. Although previous phylogenetic studies have advanced understanding of the evolutionary history of Androsace , its biogeographic origins and diversification history have remained unresolved due to limited species sampling and low statistical support. Here, we revisited the inter‐ and infrageneric taxonomic controversies. Using chloroplast genome (cpDNA) and nuclear ribosomal ITS (nrDNA) sequences from 101 species representing four related genera and seven infrageneric sections, we reconstructed the most comprehensively sampled phylogeny of Androsace to date and established a spatiotemporal framework for its biogeographic and diversification history. Phylogenetic analyses based on cpDNA revealed four well‐supported clades corresponding to distinct ecological, geographic, and morphological traits. A similar four‐clade structure was recovered in the ITS phylogeny, albeit with lower statistical support. Divergence time estimation and biogeographic analyses traced the origin of Androsace s.l . to the Pan‐Tibetan Highlands in the early Oligocene (~33 Ma), identifying this region as the source for other mountain systems. The genus underwent asynchronous diversification across different mountain systems and clades, driven by distinct tectonic events, environmental changes, and trait innovations. These results provide a spatiotemporal framework for understanding the evolution of alpine plants in the Northern Hemisphere.

BACKGROUND AND AIMS:Species identification in polyploid plants remains challenging owing to morphological continuity and genomic redundancy. Such taxonomic uncertainties obscure evolutionary or ecological inference. A critical solution involves the reassessment of polyploid collections using stable diagnostic traits and integrative approaches. Here, we examined the Rorippa dubia-indica complex (Brassicaceae), a morphologically overlapping tetraploid-hexaploid lineage with a native distribution in East Asia. METHODS:We developed a framework that integrates experimental phenotyping, herbarium reassessment and computational modelling for secondary species assessment of polyploid plants. The framework incorporates spatiotemporal data from 3136 field-collected (2017-2020) and 2015 herbarium (1893-2021) specimens. Species were circumscribed using experimental assessments of anatomical, cytological and morphological traits, interpreted within a phylogenetically informed evolutionary context. Stable diagnostic traits were then applied to re-identify specimens for improved species distribution models. Finally, curated trait and species data were used to train machine learning classification models to reconstruct the diagnostic rationale underlying specimen identification. KEY RESULTS:Seed arrangement, number of petals and genome size exhibited clear interspecific differentiation. Phylogenomic analyses based on chloroplast genomes further resolved species circumscription consistent with these traits. According to the revision of specimens and classification models defined by machine learning, we found that initial misidentification rates reached 12-50 % across virtual or physical specimens, largely owing to reliance on plastic traits, such as leaf shape. These errors substantially distorted spatial distribution models and future climate projections. CONCLUSIONS:Our findings underscore the need for secondary specimen evaluation. The framework demonstrates the importance of integrating morphological and phylogenetic inference with machine learning tools to resolve taxonomically difficult polyploid complexes. This approach offers direct applications for biodiversity assessment, evolutionary research and conservation planning.

Abundant and exceptionally preserved Tilia macrofossils from the Early–Middle Miocene of the Korea provide a rare organ-level assemblage that includes flowers, fruits (nutlets), bracts, and leaves from the same flora. Notably, the material represents the first confirmed fossil flower of Tilia, preserved with a beaker-shaped perianth and diagnostic internal lamellae, enabling confident floral–androecial interpretation. Systematic study documents two new species—T. pentagona sp. nov., characterized by a Type C leaf-like bract and a ribbed, mamillate nutlet with a pentagonal cross-section, and T. perpendicularis sp. nov., based on the well-preserved flower—and further assigns additional organs to T. tomentosella, T. asiatica, and T. miohenryana. In contrast to the two native species (T. amurensis and T. mandshurica) present in Korea today, our findings demonstrate that Miocene Korea supported a richer Tilia assemblage than today. A historical biogeographical synthesis, informed by the stratigraphic distribution of Tilia fossils and deep-time ecological niche modeling, indicates that suitable habitats encompassed Korea during the Miocene but contracted markedly thereafter, consistent with the Quaternary cooling. Together, our findings enrich the fossil record of Tilia and reveal that the favorable Miocene climates in Korea fostered a higher diversity of the genus.

The Grant-Stebbins model predicts that a plant species encountering different pollinators across its range may undergo local adaptation and, subsequently, ecological speciation. We tested whether this could explain the origin of Aeschynanthus acuminatus (Gesneriaceae), a species phylogenetically derived from sunbird specialist ancestors. A. acuminatus is widespread throughout mainland E Asia but also occurs in Taiwan, beyond the range of sunbirds, where it is pollinated by generalist passerines. We hypothesized that A. acuminatus originated from an ancestral lineage that colonized Taiwan, rapidly adapted to its novel pollinator fauna, and secondarily spread to the mainland. We tested among evolutionary scenarios by integrating studies of phylogeography, pollination, and floral morphology. Phylogeographic analysis of genome-wide SNPs revealed a mainland origin. Pollinator observations showed varied visitation by both sunbirds and generalist passerines across mainland Asia. The origin of A. acuminatus likely involved a pollinator niche expansion to include generalist passerines, an ecological shift that enabled its subsequent range expansion. Hypothetical pollinator-mediated fitness models suggest that the derived floral morphology of A. acuminatus represents an adaptive optimum for generalist passerine pollination rather than an intermediate phenotype. Our research illustrates how the evolution of pollinator niches can influence the origin and range dynamics of plant species.

Koenigia medogensis, a distinctive new species discovered in Medog County, southeastern Xizang, China, is here described and illustrated. The generic placement of this species was validated through integrated morphological and palynological observations, as well as molecular phylogenetic analyses using three cpDNA markers (matK, rbcL, and trnL-F). Within Koenigia, K. medogensis is most closely related to K. mollis but differs significantly in growth habit, leaf shape, inflorescence structure, and achene micromorphology. Crucially, K. medogensis possesses a unique vegetative reproductive strategy, viz. the production of bulbils at both stolon apices and inflorescence apex. This dual-bulbil trait is exceptionally rare within Polygonaceae and likely represents an evolutionary adaptation to the hyperhumid monsoon environment of Medog County as a reproductive assurance strategy.

Genome size exhibits substantial variation across organisms, but its causes and ecological consequences remain incompletely understood. While interspecific comparisons have suggested selective pressures against large genomes, intraspecific variation has been less explored. Here, we investigate genome size diversity within the hexaploid yellowcress Rorippa indica by integrating flow cytometry, plastome phylogeography, genomic repeat profiling, and reciprocal common garden experiments. Across 192 accessions from 83 natural populations, genome size ranged from 764 to 892 Mb, a 15.8% difference relative to the mean (812 Mb), representing the widest range yet reported within Rorippa. Plastome haplotype analysis revealed that lineages colonizing tropical habitats tended to retain or enlarge genome size, whereas northern lineages exhibited reductions. Genome size was significantly correlated with tropical environments characterized by higher winter temperatures and reduced seasonality. Variation was largely attributable to repetitive DNA, with 45S rDNA and Ty1-copia retrotransposons (Bianca) explaining up to 15.5% and 26.1% of the differences, respectively. Reciprocal transplantation experiments demonstrated that plants with larger genomes had higher fitness in tropical conditions, producing 32% more fruits. These findings indicate that genome size in R. indica is not a neutral trait but is selectively expressed, with both shrinkage and enlargement representing adaptive strategies under contrasting environments. We propose that genome enlargement, driven primarily by specific repetitive elements, constitutes an adaptive response to stable tropical climates. As global warming progresses, species with larger genomes may exhibit slower growth but increased reproductive output, with broad implications for ecosystem dynamics and agricultural productivity.

Angiosperms are the most diverse and abundant plant taxon today and dominate the majority of Earth's terrestrial ecosystems. They underwent rapid divergence and biogeographic expansion from the early to the middle Cretaceous. Yet, transformative ecosystem change brought about by the increased ecological dominance of angiosperms unfolded progressively until the Late Cretaceous. After the Cretaceous-Paleogene (K-Pg) boundary, angiosperms restructured terrestrial ecosystems towards a modern form. By the Neogene, crown groups that make up modern terrestrial angiosperm biodiversity radiated, and regional floristic distinctions were established concurrently with the steepened latitudinal and vertical temperature gradients. Here, we summarize, based on fossils and molecular evidence, when and how angiosperms came to diversify, dominate, and shape terrestrial ecosystems, leading to the emergence and spread of angiosperm-dominated floras. We highlight five major phases of angiosperm evolution that took place against a background of palaeogeography and climate changes. There is a consistent delay in ecological dominance after lineage origination and taxonomic diversification, as a result of which angiosperms did not achieve ecological dominance across terrestrial biomes in a single step. The patterns of diversity seen among extant angiosperms, the dominant angiosperm groups within modern ecosystems, and the restriction of different groups of angiosperms to different parts of the world, reflect the contingent nature of the process of lineage diversification in the context of long-term, substantial and ongoing environmental change. Determining the origins, diversification, and ecological dominance of angiosperms continues to be a challenge and requires elucidation of their early forms, functions, habitats, and environmental interactions throughout evolutionary history.

Understanding how biotic assembly processes responded to past geoclimatic changes is key to explaining the origins of mountain biodiversity and the causes of regional disparities in species richness. Here, we jointly reconstructed geographic ranges and biome-niche evolution for 34 diverse plant clades across five major Northern Hemisphere mountain systems and quantified how late Neogene cooling increased arctic-alpine habitat connections across regions. We reveal that, while alpine floras originated asynchronously and were assembled through distinct evolutionary processes over the past 30 million years, general biological responses to orogeny and environmental change are apparent. Across regions, in situ diversification was consistently elevated during heightened phases of tectonic activity. Over the past 5 million years, enhanced arctic-alpine connectivity facilitated biotic interchange and positioned the boreal-arctic region as a major biogeographic crossroads linking Eurasia and North America.

Species delimitation in polyploid complexes remains a fundamental challenge due to pervasive morphological overlap and genomic redundancy. We examined the Rorippa dubia–indica complex (Brassicaceae), a polyploid lineage comprising tetraploid and hexaploid taxa. We developed an integrative 3D framework (Delimitation, Distribution, and Decoding) that synthesizes spatiotemporal data from field (2017–2020; n = 3,136) and herbarium (1893–2021; n = 2,015) collections to diagnose misidentification, model distributions, and reconstruct classification criteria used in polyploid complexes. Morphological traits with varying degrees of plasticity were evaluated under controlled conditions to identify stable diagnostic characters. Seed arrangement, petal number, and genome size or ploidy level exhibited clear interspecific differentiation. Phylogenomic analyses based on chloroplast genomes further defined species boundaries clarified by these taxonomic traits. We then revised herbarium specimens and applied machine learning classification models to assess the extent of specimen misidentification and to recover the trait-based rationale behind species assignments. Initial misidentification rates reached 12–50% across virtual or physical specimens, largely due to reliance on plastic traits. These errors substantially distorted spatial distribution models and future climate projections. Our findings underscore the need for secondary specimen evaluation and demonstrate the importance of integrating morphologic and phylogenetic inference with machine learning tools to resolve morphologically overlapping polyploid complexes. This approach offers direct applications for biodiversity assessment, evolutionary research, and conservation planning. ### Competing Interest Statement The authors have declared no competing interest. National Natural Science Foundation of China, 32170224, 32225005 National Key Research and Development Program of China, 2024YFF170140203

Phytolith analysis of pteridophytes (ferns and lycophytes) is significant for reconstructing paleoenvironments and understanding their evolutionary histories. However, current research on phytoliths in extant pteridophytes remains scarce compared to these for angiosperms. This study focused on the highly diverse pteridophytes in Xishuangbanna, a tropical region in East Asia, and 20 species from 16 genera of pteridophytes were collected for this study. The morphology and production of their phytoliths were observed in detail, and a statistical analysis was conducted. Results revealed significant differences in both the production and morphology of phytoliths among species. Nine genera were identified as typical phytolith producers, with a total of 27 distinct morphotypes. We also identified potential diagnostic morphotypes of phytolith with taxonomic significance in 10 species. Among them, EPIDERMAL OVATE ORNATE and CYLINDRICAL VERRUCATE exhibited distinct characteristics and were produced in high quantities within plants, making these phytoliths the most promising morphotypes for classification. Meanwhile, the phytolith data encompassing 258 pteridophyte species was amassed in the present study. This study increased new information on the morphology of pteridophyte phytoliths in tropical regions, thereby offering pivotal insights for the utilization of pteridophyte phytoliths in research fields such as taxonomy, archaeology, and paleoecology.

Despite the significance of Gnetales in understanding the origin and evolution of seed plants, the morphological diversity of ancestral forms within this group remains unclear, and the evolutionary processes affecting their vegetative and reproductive structures lack robust evidence. In this study, we describe a new ephedroid macrofossil from the Lower Cretaceous Yixian Formation in western Liaoning, China. This species is characterized by decussate phyllotaxy, internodes with fine longitudinal striations, swollen nodes, and female cones featuring paired bracts and one to two seeds. While these characteristics resembled extant Ephedra, there are notable morphological differences, including oppositely branched stems of equal length and a seed envelope with transversely aligned epidermal cells on its surface. Consequently, we designate this new macrofossil reproductive shoot as a new species, Ephedra transversa sp. nov.. The findings of this study support the reduction and sterilization hypothesis and enhance our understanding of the evolutionary processes within Gnetales.

Evergreen broad-leaved forests (EBLFs) are widely distributed in East Asia and play a vital role in ecosystem stability. The occurrence of these forests in East Asia has been a subject of debate across various disciplines. In this study, we explored the occurrence of East Asian EBLFs from a palaeobotanical perspective. By collecting plant fossils from four regions in East Asia, we have established the evolutionary history of EBLFs. Through floral similarity analysis and paleoclimatic reconstruction, we have revealed a diverse spatio-temporal pattern for the occurrence of EBLFs in East Asia. The earliest occurrence of EBLFs in southern China can be traced back to the middle Eocene, followed by southwestern China during the late Eocene–early Oligocene. Subsequently, EBLFs emerged in Japan during the early Oligocene and eventually appeared in central-eastern China around the Miocene. Paleoclimate simulation results suggest that the precipitation of wettest quarter (PWetQ, mm) exceeding 600 mm is crucial for the occurrence of EBLFs. Furthermore, the heterogeneous occurrence of EBLFs in East Asia is closely associated with the evolution of the Asian Monsoon. This study provides new insights into the occurrence of EBLFs in East Asia.

Global climate change poses a severe threat to mountain biodiversity. Phenotypic plasticity and local adaptation are two common strategies for alpine plant to cope with such change. They may facilitate organismal adaptation to contrasting environments, depending on the influences of the environment or genotype or their interacted effects. In this study, we use an endemic alpine plant (Rorippa elata) in the Hengduan mountains (HDM) to unravel its phenotypic basis of adaptation strategy and evaluate the relative contributions of environment and genotype to its phenotype. We transplanted 37 genotypes of R. elata into two common gardens across low and high elevations (2800 vs. 3800 m) during 2021-2022. Nine fitness-related traits were measured, including flowering probability and glucosinolates (GS) content. We estimated the environmental or genotypic contributions to the phenotype and identified the main environmental components. Our results revealed that both environment and genotype-by-environment interactions contributed to the phenotypes of R. elata. Latitudinal heterogeneity was identified as a key factor that explained 24% of the total phenotypic variation. In particular, genotypes of the northern HDM showed significantly higher plasticity in flowering probability than those of the southern HDM. Furthermore, within the southern HDM, GS content indicated local adaptation to herbivory stresses for R. elata genotypes along elevations. In conclusion, our results suggest that R. elata may have adapted to the alpine environment through species-level plasticity or regional-level local adaptation. These processes were shaped by either complex topography or interactions between genotype and mountain environments. Our study provides empirical evidence on the adaptation of alpine plants.

AimLong-distance dispersal (LDD) plays an important role in shaping the distribution of global biodiversity. Polyploidy could favour invasion and thereby facilitate LDD. However, how and to what extent polyploidy interacts with LDD remain unclear. Here, we test the putative role of polyploidy in the global dispersal of a cosmopolitan genus Rorippa.LocationGlobal.Time PeriodLate Miocene to present.Major Taxa StudiedRorippa Scop., Brassicaceae.MethodsWe traced the biogeographical and speciation history for 17 diploids and 41 polyploids of Rorippa using variation from plastid genomes and multiple nuclear loci. The ploidy role in dispersal rate difference was demonstrated using trait-dependent biogeographical modelling.ResultsLDD shaped the amphitropical disjunction of Rorippa, during which polyploids showed higher dispersal rates than those of diploids, with 5.6x increase under the best-fitted model. Five diploids and 21 polyploids were identified as products of transoceanic speciation events. Polyploidy-involved LDD was more common in terms of polyploidization following LDD than those preceding LDD.Main ConclusionsWe demonstrate that polyploidy would be not only a driver but also a responder of LDD in Rorippa, highlighting a synergistic relationship between them. Our results provide a framework to uncover the biogeographical consequences of polyploidization and the joint roles of polyploidy and LDD in shaping the distribution of biodiversity.

While the genome sizes of flowering plants vary c. 2400-fold, it remains little known what factors may have driven the variation. In this study, we investigated the spatial pattern of the genome size of 54 populations of Acanthocalyx , which is found in the Hengduan-Himalaya Mountains. Our results showed that the red-flowered lineage of Acanthocalyx had significantly larger genomes (ranging from 1.9 to 2.5 Gb) compared to the white-flowered lineage, which had an average genome size of 1.27 Gb. This difference in genome size can be attributed to particular environmental factors. Within the red-flowered lineage, the genome size was positively correlated with soil nitrogen content and mean diurnal range. On the other hand, the genome size of the whiteflowered lineage, Acanthocalyx alba was negatively correlated with latitude which aligns with the population dynamics of this species during the Pleistocene. Overall, our findings highlight the influence of abiotic factors and geography in regulating the genome size of Acanthocalyx species. This study contributes to our understanding of the evolution of alpine plants in the HengduanHimalaya Mountains.