The Pan-Himalaya, known as the “Roof of the World”, forms a natural geographic unit covering the entire range of the Himalaya and the Hengduan Mountains in addition to Karakorum and the northeastern extreme of Hindu Kush. The region possesses three biodiversity hotspots and harbors a rich and distinctive flora. Here, we review the history of plant diversity surveys and monographic studies in the region. The contributions of outstanding collectors of Pan-Himalaya are also reviewed, as well as the ongoing international project on the Flora of Pan-Himalaya (FPH). As the main concern of the present review, we showed that the development of botanic survey is uneven among different areas in the Pan-Himalaya region, and that a special concern should be given to northern Myanmar and Yarlung Zangbo–Brahmaputra.

Pan-Himalaya, including Himalaya and its neighboring areas, hosts a rich and unique flora that is crucial for understanding the evolutionary history of mountainous biodiversity. Phylogenetic regionalization can provide novel insights into biodiversity distribution patterns and their formation mechanisms. In this study, based on comprehensive species distribution data and a species-level phylogenetic tree, we propose a phylogenetic regionalization scheme of the Pan-Himalayan vascular flora comprising 15 zones, which can be grouped into five floristic subregions and three floristic regions (i.e., the West Himalayan [WH], the Southeast Himalayan [SEH], and the Northeast Himalayan [NEH] regions). Our results reveal that the SEH and NEH regions are closely clustered, which are then grouped with the WH region. The floras of these three regions exhibit distinct evolutionary histories and phylogenetic structures. The WH region presents a phylogenetically clustered flora with Euro-Mediterranean affinities and the highest evolutionary uniqueness. The NEH region has the highest species richness and phylogenetic diversity, with most of its areas, especially at higher elevations, displaying phylogenetic clustering. In contrast, the SEH region exhibits a phylogenetically overdispersed flora, characterized by harboring species-rich families with tropical, temperate, and alpine distributions, as well as relict plant lineages. This study provides valuable insights into the evolutionary history of the Pan-Himalayan flora and informs the development of effective conservation strategies.

The formation of the Qinghai–Tibet Plateau has long been debated, despite the various proxies used to estimate its paleoelevation. Here, we introduce a novel method to calibrate paleoelevation by comparing the fossil and extant plant communities in the Qinghai–Tibet Plateau. Our estimation confirms that the uplift of the plateau was an episodic and heterochronous process. Specifically, the Lhasa Terrane was already elevated by 1 km before the initial India–Asia collision. During the first orogenic stage, the Qiangtang Terrane rose faster than the Lhasa Terrane, attaining 3 km in the late Eocene. In the second stage, the Lhasa Terrane underwent rapid uplift, reaching 3 km in the Oligocene. By the Middle Miocene, both the Qiangtang and Lhasa terranes had achieved an elevation of 4 km. The Himalaya rose by at least 2 km after the Pliocene. Our biological knowledge-based findings contradict the previous geological evidence-based reports, which posited that the plateau had reached an elevation of 4–5 km during the Eocene. We provide a new perspective on the plateau’s uplift history based on biological evidence, which has the potential to reconcile the confusion arising from contradictory proxies.

Understanding the Cenozoic vegetation history of what is now the Qinghai–Tibetan Plateau is crucial for elucidating the co-evolutionary dynamics between plateau development, its environment, and the organisms it hosts. In this study, we conduct a comprehensive analysis of phytoliths within the late Oligocene–Early Miocene lacustrine sedimentary section of the Lunpola Basin, central Qinghai–Tibetan Plateau. The diverse phytolith morphotype assemblages indicate that the vegetation of the central Tibetan region mainly comprised a mixed coniferous and broad-leaved forest. Grasses in the understory primarily consisted of Pooideae, distinguished by phytolith morphotypes such as rondel, crenate and Stipa-type bilobate forms. Combined with previous work, we infer that riparian vegetation of the central Tibetan region transitioned from a humid subtropical forest, dominated by broad-leaved woody plants during the middle Eocene, to a more seasonally arid open woodland containing abundant woody and herbaceous plants during the late Eocene, before developing into a cooler mixed coniferous and broad-leaved forest during the late Oligocene–Early Miocene. The growth of the central Tibetan region and retreat of the Tethys Ocean, together with the uplift of the Himalaya, contributed to this vegetation change. This study provides new evidence from the phytolith perspective for the evolutionary history of Qinghai–Tibetan Plateau vegetation being tied to plateau formation and regional climate change.

The uplift of the Qinghai-Tibet Plateau shaped the landforms and influenced Asia’s climate system and ecosystem. Vegetations on the Plateau are the first to be affected by the uplift history of the Qinghai-Tibet Plateau and related ecological impacts. However, original research on vegetation in the central Qinghai-Tibet Plateau remains limited. Here, we reconstructed the vegetation in the Lunpola Basin, central Qinghai-Tibet Plateau from 24.3 to 16 Ma based on pollen data from the Dingqinghu Formation. Pollen assemblages reveal a temperate mixed deciduous broad-leaved and coniferous forest around the Lunpola paleolake during the latest Oligocene to the Early Miocene. An obvious vegetation vertical zone existed near the Lunpola Basin. Dark coniferous forests grew in the highlands, thermophilous shrubs stayed in the lowlands. This work provides new and original data on plant composition and vegetation in the central Qinghai-Tibet Plateau and enhances our understanding of the ecological impacts of the Qinghai-Tibet Plateau uplift.

For clades originating in warm climates, the tropical niche conservatism hypothesis predicts that current biological assemblages in colder or drier climates are expected to have lower phylogenetic diversity, and species in colder or drier climates are expected to be more closely related to each other (i.e., higher phylogenetic clustering). Liverworts are one of the oldest clades of extant land plants. They originated about 500 Ma during a warm (“greenhouse”) period and experienced multiple major cycles of warm and cold periods. Here, I test the tropical niche conservatism hypothesis using liverwort assemblages distributed along an elevational gradient crossing about 5000 m of elevation in the central Himalaya. I found that, in general, phylogenetic diversity and dispersion decrease with increasing elevation and thus with decreasing temperature, which is consistent with the tropical niche conservatism hypothesis. Phylogenetic diversity decreases with elevation monotonically, but phylogenetic dispersion decreases with elevation in a triphasic (zig-zag) pattern, which is generally consistent with the triphasic pattern found in angiosperms and polypod ferns along the same elevational gradient. Temperature-related variables explained approximately the same amount of the variation in phylogenetic diversity and dispersion as did precipitation-related variables, although mean annual temperature explained 9%−15% more variation than did annual precipitation. Climate extreme variables explained approximately the same amount of variation in phylogenetic diversity and dispersion as did climate seasonality variables.

Tongoloa is a herbaceous genus of East Asia Clade (Apiaceae) distributed in the alpine regions. The use of DNA fragments has not provided a well-resolved evolutionary history. For this research, we primarily collected samples from the type localities of Tongoloa and closely related taxa in the Hengduan Mountains. The chloroplast (cp) genomes and nuclear ribosomal (nr) DNA repeats of 27 taxa were assembled using genome skimming sequencing reads. We analyzed the characteristics of the Tongoloa cp genome, and found a remarkable expansion of the Inverted Repeats. Three genes (ndhC,  ndhJ, and petG) related to photosynthesis appear to have undergone significant selective pressure. Through high-resolution phylogenetic analysis, the cpDNA provided compelling evidence supporting the inclusion of Sinolimprichtia as an early taxon within Tongoloa. However, the nrDNA suggested that Tongoloa and Sinolimprichtia belong to distinct branches. Morphological analysis showed that Tongoloa has broadly oval fruits with a cordate base, whereas the fruits of Sinolimprichtia are long-obovate with an obtuse base. The specific fruit morphology of Sinolimprichtia was found to be nested within Tongoloa in the cpDNA phylogenetic tree. Ancient introgression and chloroplast capture provide the most plausible explanation for the significant conflict between the nrDNA and cpDNA phylogenies. Our study highlights the potential impact of the complex evolutionary history of Tongoloa on the challenges encountered in previous taxonomic treatments.

Understanding plant diversity and the phylogenetic divergences in the Northern Hemisphere is essential for in-depth evolutionary studies and conservation efforts. Maianthemum is an ideal example to explore plant diversification processes in the Northern Hemisphere, with more than 35 species widely distributed in forests in North to Central America, Europe and eastern Asia. Yet the phylogenetic relationships within Maianthemum remain elusive. In this study, we reconstructed a well-supported phylogenetic framework of Maianthemum and explored possible gene introgressions and reticulate evolution using nuclear and chloroplast genomes based on the target enrichment Hyb-Seq approach. Both nuclear and chloroplast phylogenetic results supported three clusters corresponding to their biogeographic distribution of the New World, the Himalayan-Hengduan Mountains, and the north temperate zone, respectively. The genus was inferred to be most likely originated in North America with migrations into Central America and eastern Asia in the late Miocene. Our results suggested that both incomplete lineage sorting and hybridizations/introgressions along with geographic isolation have contributed to the rapid divergence of Maianthemum in eastern Asia, which may represent a complex model for the evolutionary radiation of plants in eastern Asia and even the Northern Hemisphere.

Panax (Araliaceae) is a small genus containing several well known medicinally important species. It has a disjunct distribution between Eastern Asia and Eastern North America, with most species from eastern Asia, especially the Himalayan-Hengduan Mountains (HHM). This study used the genomic target enrichment method to obtain 358 nuclear ortholog loci and complete plastome sequences from 59 accessions representing all 18 species of the genus. Divergence time estimation and biogeographic analyses suggest that Panax was probably widely distributed from North America to Asia during the middle Eocene. During the late Eocene to Oligocene Panax may have experienced extensive extinctions during global climate cooling. It survived and diverged early in the mountains of Southwest China and tropical Indochina, where some taxa migrated northwestward to the HHM, eastward to central and eastern China, and then onward toward Japan and North America. Gene flow is identified as the main contributor to phylogenetic discordance (33.46%) within Panax. We hypothesize that the common ancestors of the medicinally important P. ginseng + P. japonicus + P. quinquefolius clade had experienced allopolyploidization, which increased adaptability to cooler and drier environments. During the middle to late Miocene, several dispersals occurred from the region of the HHM to contiguous areas, suggesting that HHM acted as a refugium and also served as a secondary diversification center for Panax. Our findings highlight that the interplay of orographic uplift and climatic changes in the HHM greatly contributed to the species diversity of Panax.

Adaptive radiation is usually triggered by great in situ or ex situ environmental changes. How an adaptive radiation occurs on lands and how species richness relates to morphodisparity have been a major focus of evolutionary biology. Petrocodon, diversified in the southeastern Qinghai–Tibet Plateau (QTP), represents an ideal model to address these questions. To elucidate the dynamics of adaptive radiation of Petrocodon, we took an integrative approach, including phylogenetic, dating, disparity versus diversity, pollination, and gene expression analyses. Petrocodon with six clades has experienced radiation following the QTP uplift. Multiple modes of floral morphodisparity versus species diversity occur in the radiation process that are directly linked to their colonizing new environments and diversification with geographic expansion. Pollination and gene expression analyses suggest that accelerated emergence of de novo mutations might be relevant to the multiplex floral disparity and pollinator shifts in Petrocodon. For the first time in plants, we report that decreased genetic constraints on floral architecture triggered by QTP uplift might have generated abundant floral morphological variants, which were further targeted by selection for ecological divergence. The multiple modes of floral disparity versus species diversity may be attributed to accelerated mutations in colonizing new environments and repeated modifications of the already evolved traits in subsequent diversification and geographic expansion in Petrocodon. Our findings shed novel light on the interplay of ecological, developmental and evolutionary dynamics of disparity versus diversity in relation to trajectory changes of floral architecture in responses to environmental disturbance in a terrestrial plant group.

The Himalayas represent a complex mountain system housing some of the world’s richest floras along with a high level of endemism. Among them,  Lysionotus (Gesneriaceae) stands out as a small genus (∼34 species) that is unexpectedly distributed across southern to eastern Asia. Within this genus, the mountain forests of the south Pan-Himalaya region emerge as a hotspot of diversity, hosting most epiphytic and endemic Lysionotus species. To explore the origin, evolutionary history and development of the current distribution pattern of Lysionotus, we inferred a highly resolved phylogenetic framework using 649 nuclear genes sourced from transcriptomes for 27 species. We revealed three major clades within Lysionotus with strong support, corresponding to the genus’s classification into three sections (sects. Didymocarpoides,  Lysionotus, and Cyathocalyx) based on morphological characters. Molecular dating suggests that Lysionotus is likely to have originated in the karst regions of northern Vietnam to southwestern China during the middle Oligocene (28.18 Ma), and then migrated westward to the southern Himalaya regions during the Miocene. The speciation rates of Lysionotus were likely to be positively linked to changes in East Asian monsoons and past temperatures. Notably, epiphytic species of sect. Lysionotus began colonizing the tropical and subtropical forests of the Pan-Himalaya around the mid-Miocene Climatic Optimum, coinciding with the transition to long seed appendages. Our findings support that the formation and development of forests in the southern Himalaya, along with paleo-climate changes and morphological innovations, which probably facilitated the evolution and expansion of the spatial distribution of Lysionotus.

The loss of biodiversity is one of the most serious environmental issues in the Anthropocene. Understanding the extinction risk of species is essential for preemptive conservation measures, but is hampered by gaps in geographical and evolutionary knowledge, especially in areas/regions that are highly diverse in species. Combined with a 21 109-taxon angiosperm mega-phylogeny and comprehensive species distribution database, we evaluated the characteristics of angiosperm extinction risk at the Sino-Himalaya and the Tibetan Plateau (SHTP). Overall, our results show that there is a strong interaction between evolutionary and environmental factors on extinction risk, and both contribute spatially to threat processing in the SHTP. The extinction risk of angiosperms in this region is spatially and phylogenetically clustered; the clades with low species richness are significantly more vulnerable to extinction than species-rich ones; the regions with the highest extinction risk are concentrated in the mountainous areas of southwest China. Integrated with the existing Red List, we further delineated more than 3000 potentially threatened species and proposed practical conservation priorities for four types of species in the SHTP. The extinction risk of angiosperms showed both phylogenetically and spatially aggregate characteristics, serving as an important reference for predicting extinction trends and the formulation of targeted conservation strategies.

Taxonomy of Populus is a challenging task, especially in regions with complex topography, such as the Qinghai–Tibet Plateau because of the effect of hybridization, incomplete lineage sorting, phenotypic plasticity, and convergence. In the Flora of China,  Populus pseudoglanca and Populus wuana are classified into sect. Leucoides and sect. Tacamahaca, respectively, but their taxonomy remains unclear. By conducting a systematic investigation for all taxa of Populus on the plateau, we found 31 taxa from the two sections. Through identification based on morphology and habitats, we confirmed that the “P. pseudoglanca” recorded in the Flora of Sichuan is not true P. pseudoglanca, while P. pseudoglanca and P. wuana recorded in the Flora of China may refer to the same species. By performing whole-genome re-sequencing of 150 individuals from the 31 taxa, we derived 2.28 million single nucleotide polymorphisms (SNPs). Further genetic and phylogenetic analyses demonstrated that the genetic structure of P. wuana is extremely consistent with P. pseudoglanca, and they all originate through the natural hybridization between Populus ciliata in sect. Leucoides and Populus curviserrata in sect. Tacamahaca. Our results suggested that P. wuana should be merged with P. pseudoglanca taxonomically. This study not only clarifies the taxonomic confusions related to P. pseudoglanca and P. wuana but also provides a new framework based on the integration of morphology, distribution, habitat, and genome to solve complex taxonomic problems.

Dipelta Maxim. (Caprifoliaceae) is a Tertiary relic genus endemic to China, which includes three extant species,  Dipelta floribunda, Dipelta yunnanensis, and Dipelta elegans. Recent progress in the systematics and phylogeographics of Dipelta has greatly broadened our knowledge about its origin and evolution, however, conflicted phylogenetic relationships and divergence times have been reported and warrant further investigation. Here, we utilized chloroplast genomes and population-level genomic data restriction site-associated DNA-single nucleotide polymorphisms (RAD-SNPs) to evaluate the interspecific relationships, population genetic structure and demographic histories of this genus. Our results confirmed the sister relationship between D. elegans and the D. yunnanensis–D. floribunda group, but with cyto-nuclear phylogenetic discordance observed in the latter. Coalescent simulations suggested that this discordance might be attributed to asymmetric “chloroplast capture” through introgressive hybridization between the two parapatric species. Our fossil-calibrated plastid chronogram of Dipsacales and the coalescent modeling based on nuclear RAD-SNPs simultaneously suggested that the three species of Dipelta diversified at the late Miocene, which may be related to the uplift of the eastern part of Qinghai–Tibet Plateau (QTP) and adjacent southwest China, and increasing Asian interior aridification since the late Miocene; while in the mid-Pleistocene, the climatic transition and continuous uplift of the QTP, triggered allopatric speciation via geographical isolation for D. floribunda and D. yunnanensis regardless of bidirectional gene flow. Based on both plastid and nuclear genome-scale data, our findings provide the most comprehensive and reliable phylogeny and evolutionary histories for Dipelta and enable further understanding of the origin and evolution of floristic endemisms of China.