During the Cretaceous period, the lacewing superfamily Mantispoidea, with an assemblage of species possessing raptorial forelegs, have undergone a rapid species radiation, characterized by abundant species richness and high morphological plasticity. Nevertheless, the morphology and early evolution of the specialized predatory organ around the time of its origin in raptorial Mantispoidea have been poorly documented due to the rarity of fossil evidence, especially for the pre-Cretaceous fossils. Herein, a new genus and new species, that is Archarhachiberotha longitarsa Wang, Ren et Wang gen. et sp. nov., was described from the Middle Jurassic Jiulongshan Formation of northeastern China. This new genus was characterized by the remarkable raptorial forelegs, that is, typically elongated coxa, relatively less-swollen femur and rudimentary small femoral spines, and well-developed tarsi. Considering the peculiar morphological combination and antiquity of the new genus, it was assigned to be a stem-group lineage of Mantispoidea. Also, the detailed analyses of morphology and biological functions of raptorial forelegs were made to conclude that the new genus evolved into an unknown but primitive raptorial type that was distinctly different from the extant morphological features and raptorial mechanisms. In addition, the evolutionary tendency of raptorial Mantispoidea herein summarized highlights morphological diversity and disparity between fossil and extant representatives, and provides a rare case to explore the entire evolutionary history of a specialized structure in one lineage.

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.

Speciation events often occur with adaptive radiation. The factors that promote these adaptive radiating species diversity patterns have intrigued biologists for more than a century. In the present study, we used the adaptive radiated genus Ligustrum to evaluate the relative contributions of the environment, species interactions, phylogenetic diversity, and diversification rates in generating extant species diversity patterns. Using complete chloroplast genome data, we reconstructed the highly supported and dated backbone phylogenetic relationships of Ligustrum. Biogeographic results indicated that Ligustrum originated in Southwest China during the Oligocene and spread to suitable areas that were warm and humid via 18 dispersal events. For the overlapping ranges of species pairs, a smaller phylogenetic distance was detected in high species overlap than in low species overlap, which is consistent with no significant difference in niche among the different species. We found that the phylogenetic diversity and interspecies competition induced by insignificant niche divergence shaped the global pattern of Ligustrum diversity.

We describe a new species of Ampelopsideae (Vitaceae), Nekemias mucronata sp. nov., from the Rupelian of Cervera (Spain) and revise another fossil species, Ampelopsis hibschii, originally described from Germany. Comparison with extant Ampelopsideae suggests that the North American species Nekemias arborea is most similar to Nekemias mucronata while the East Mediterranean Ampelopsis orientalis is the closest living relative of A. hibschii. Our review of fossil data indicates that, during the Eocene, four species of Ampelopsideae occurred in Eurasia, that is, N. mucronata in the Czech Republic, A. hibschii in Kazakhstan, and two fossil species in the Far East (Ampelopsis cercidifolia and Ampelopsis protoheterophylla). In the Oligocene, a new species, Ampelopsis schischkinii, appeared in Kazakhstan; meanwhile, N. mucronata spread eastwards and southwards, and A. hibschii mainly grew in Central Europe. In the late Oligocene, N. mucronata became a relict in the Iberian Peninsula and Nekemias might have persisted in Western Eurasia until the latest Miocene (“Ampelopsis” abkhasica). The last occurrence of A. hibschii was in the Middle Miocene in Bulgaria, probably a refuge of humid temperate taxa, along with Ampelopsis aff. cordata. Carpological remains suggest that this lineage persisted in Europe at least until the Pleistocene. Our data confirm previous notions of the North Atlantic and Bering land bridges being important dispersal routes for Ampelopsideae. However, such dispersion probably occurred during the Paleogene rather than the Neogene, as previously suggested. A single species of Ampelopsideae, A. orientalis, has survived in Western Eurasia, which appears to have been linked to a biome shift.

The daisy tribe Anthemideae Cass. is one of the largest and most diverse tribes within Asteraceae. We analyzed a data set including 61 out of 111 Anthemideae genera, and all but four of the 19 currently recognized subtribes (Inulantherinae, Lapidophorinae, Lonadinae, and Vogtiinae) using a targeted high-throughput sequencing approach, the first focused on the tribe. We followed different phylogenomic approaches, using nuclear and plastid data, as well as additional analytical methods to estimate divergence times and diversification rates, to unravel the evolutionary history and classification of this tribe. Our results reinforce the phylogenetic backbone of the Anthemideae advanced in previous studies and further reveal the possible occurrence of ancient hybridization events, plastid capture, and/or incomplete lineage sorting (ILS), suggesting that complex evolutionary processes have played an important role in the evolution of this tribe. The results also support the merging of subtribe Physmasperminae into Athanasiinae and subtribe Matricariinae into Anthemidinae and clarify previously unresolved relationships. Furthermore, the study provides additional insights into the biogeographic patterns within the tribe by identifying three main groups: the Southern African Grade, the Asian Clade, and the circum-Mediterranean Clade. These groups partially coincide with previously identified ones. Overall, this research provides a more detailed understanding of the Anthemideae tribe and improves its classification. The study also emphasizes the importance of phylogenomic approaches for deciphering the evolutionary dynamics of large and diverse plant lineages.

Tetradium, a genus within Rutaceae, comprises nine species found in Eastern and Southeastern Asia, distinguished by their opposite pinnate leaves and apocarpous or subapocarpous gynoecium with follicular fruits. While Hartley's 1981 monograph provided foundational insights, a comprehensive phylogenetic analysis of the genus is lacking. Using next-generation sequencing (NGS), this study aims to (i) establish an NGS molecular data set for Tetradium, (ii) elucidate interspecific relationships via the hybrid capture method and (iii) investigate the taxonomic status of Euodia meliifolia var. celebica. Our data set comprised 28 samples across nine species, sequenced using Illumina Miseq and Hiseq 4000 platforms, with downstream analyses conducted using the HybPhyloMaker pipeline and ASTRAL. Our findings revealed five main groups supported by both molecular and morphological data, highlighting changes in ovule number and seed functionality. Notably, the hybrid capture method proved invaluable for studying old herbarium specimens. Finally, taxonomic revisions were proposed, including the reclassification of E. meliifolia var. celebica as Tetradium celebicum, the fossil Euodia costata as Tetradium costatum, and the fossil Euodia lignata as Tetradium lignatum. An updated description for T. celebicum, supplemented by a specific identification key, is provided.

Assessing sampling biases caused by nonrandom specimen collecting is crucial in systematics, biogeography, and conservation. Nevertheless, research on the collecting biases of vascular plants in China remains limited. Here, we investigated the collecting status of gymnosperms in China using 48 673 herbarium specimens representing 180 Chinese gymnosperm species. The spatial and temporal patterns, collector and determiner biases, and phylogenetic and taxon biases were studied to comprehend the collecting bias of gymnosperms in China during 1900–2021. Meanwhile, we assessed the inventory completeness of gymnosperms to identify collecting hotspots and coldspots. The results showed that gymnosperms predominantly inhabit mountainous areas in China. The historical collecting of gymnosperms in China can be divided into two distinct stages with four peaks of collecting activities. The distribution of collected or identified specimens per individual displays significant skewness, and the collecting of gymnosperms has the issues of overcollecting or undersampling. Inventory completeness remains deficient, and collecting intensity is weak in both northern China and the range of 22°–25° N in the southern region (i.e., central Yunnan, southern Guangxi, and eastern Guangdong). Additionally, observation of the spatial distribution reveals both hotspots and coldspots scattered across mountain regions, lacking clustering. This study revealed a highly polarized collecting pattern for gymnosperms in China. Consequently, we recommend optimizing collecting measures, targeted specimen collecting, and continuous dynamic monitoring of gymnosperms in future collecting efforts. These recommendations hold relevance not only for gymnosperms in China but also for other land plants worldwide.

The wild rats in the genus Rattus represent a group of murids characterized by rapid lineage diversification but limited morphological variation. Within this genus, there are several commensal species with high invasive capacity, such as Rattus norvegicus and R. rattus, which pose a global threat. Investigating the mechanisms behind their adaptive evolution is of utmost importance. In this study, we conducted morphological study and whole-genome sequencing on Rattus species distributed in China and adjacent regions to gain insights into morphological differentiation, as well as genomic divergence and gene flow using assembled mitochondrion genome and high-quality single nucleotide polymorphisms. Despite their morphological similarity and large overlap in morphospace, our analyses revealed significant genetic differentiation at the genomic level among Rattus species in China and adjacent regions. Specifically, intraspecific differentiation was observed in R. nitidus, R. norvegicus, and R. tanezumi, which may be related to habitat heterogeneity and geographic isolation. We hypothesize that as invasive rats expand their habitat, the diversification of ecological environments might lead to more environmentally adapted evolution and accelerated genetic differentiation. Furthermore, Dsuite and TreeMix analyses detected substantial introgression among different Rattus species, particularly evident between R. norvegicus and R. tanezumi. Strong gene flow signals suggest frequent hybridization events among these species, which may facilitate the acquisition of new environmental adaptability during their expansion into new territories. This study provides a preliminary analysis that serves as a foundation for a more comprehensive investigation into the rapid lineage diversification and adaptive introgression among Rattus species.

A full understanding of local adaptation at the genomic level will help to elucidate its role in the differentiation between closely related species. This study focused on rice seed bugs sister species (Leptocorisa chinensis and Leptocorisa oratoria), which are native to East Asia and are notorious pests targeting growing rice spikelets. East Asia is a region where diverse geology and fluctuating climate are known to have profound impacts on organisms. In this study, single nucleotide polymorphisms (SNPs) from double-digest restriction site-associated DNA sequencing and geographic distribution information were used to investigate phylogeography and assess the environmental contribution to genetic variation. We found clear genetic differentiation between sister species, but a lack of genetic structure within species because of their long-distance dispersal ability. The demographic model involved a scenario in which divergence in isolation (~0.6 Ma) was followed by secondary contact (~7 kya). The initial divergence may have been caused by the intensification of the East Asian monsoon during the Pleistocene climate oscillation. The historical demography indicated that the effective population size (N_e) showed an evident increase from 9 to 7 kya, which may be related to rice domestication and extensive human cultivation during the Holocene. We also detected a significant correlation between genetic and environmental distance, and the niche difference occupied between them. Temperature-related variables were ranked as the main factors for the difference, and 410 selective SNPs involved in adaptation were identified. The Nanling Mountains in southern China serve as a geographical boundary between them and act as an ecological barrier belt that promotes local environmental adaptation. Our study demonstrates that historical climate change and local adaptation by climate-imposed selection shape the phylogeographical patterns of sister species.

Based on several earwigfly specimens with well-preserved mouthparts of Meropeidae from mid-Cretaceous Burmese amber, a detailed, initial analysis was conducted of the structure of Mesozoic meropeids. Compared to the singularly flattened mandible of modern meropeids, the new specimens reveal that Mesozoic representatives had two distinct types of mandibles: blade-shaped and scoop-shaped. Current fossil evidence indicates that during the Mesozoic Era, Meropeidae displayed sexual dimorphism that was reflected in the structure of their mandibles. This structural difference may indicate that about 99 million years ago, meropeids had a more complex diet than extant confamilial taxa. Phylogenetic results suggest that Torvimerope gen. nov., along with Burmomerope, two extinct genera, form a clade and that are the sister taxon to crown-group Meropeidae. The new material offers new possibilities for inferring the feeding habits and mating behavior of early Meropeidae.

Ecological interactions and evolutionary processes in areas of endemism remain little studied despite the fact that identifying the patterns of functional signatures in areas of endemism could reveal important information regarding community assembly and functioning. Here, we investigated whether areas of endemism of the orchids of Megamexico are hotspots of biotic interactions by comparing the orchid–pollinator interactions with those of adjacent areas. Patterns of functional signatures and phylogenetic signal were estimated, using pollination syndromes as a proxy for functional attributes. Phylogenetic signal was estimated by coding pollinator groups for every orchid recorded. Metrics of the interaction networks and the phylogenetic signal were compared with those obtained from adjacent areas. Our results indicate that areas of endemism show higher significant differences in the phylogenetic signal compared with adjacent areas. This can be explained by the many distantly related orchid lineages sharing attributes related to pollination. Network size and robustness differed statistically between the areas of endemism and the adjacent areas. The same configuration of modules in interaction networks was found in the areas of endemism; however, remarkably, the composition of species in large genera differed in these areas. Areas of endemism harbor more orchid lineages that closely interact with many groups of insects. The southerly areas of endemism in Chiapas and Central America are prominent, with the most significant phylogenetic signal and networks metrics. Results indicate that areas of endemism for the orchids of Megamexico represent hotspots of biotic interactions. Strategies for conservation must take this biotic interaction into account.

Oleaceae, a eudicot family with great species diversity, has attracted much attention from botanists because it contains many plants with important economic, medicinal, and ornamental values. However, the history of polyploidization and ancestral genome reshuffling of Oleaceae remains unclear. Here, we clarified an Oleaceae-common hexaploidization (OCH) event occurring at ~53–61 million years ago (Ma) common in all Oleaceae plants and an Oleaceae-recent tetraploidization (ORT) event occurring at ~18–21 Ma shared by the lineages of Syringa, Olea, Osmanthus, and Fraxinus. We found that high-frequency polyploidization events drove the frequency of gene loss in Oleaceae genomes and extended the size of regions containing adjacent gene loss, thereby promoting the degree of genome fragmentation. We revealed that biased fractionation between the OCH- and ORT-produced subgenomes is likely attributed to the origin of allopolyploidization in the OCH and ORT events. Significantly, through paleochromosome rearrangement comparisons, we proposed a "two-step" genome duplication model for OCH and determined the duplicated orders of OCH tripled genome. We reconstructed 11 protochromosomes of the most recent ancestral Oleaceae karyotype (AOK) and elucidated the trajectories of immense paleochromosome reorganization of Oleaceae species from ancestral eudicot karyotype. Notably, we tracked the diversification history of secondary metabolite synthesis genes in the Oleaceae and explored the effects of paleogenome evolution on specialized metabolite synthesis. Our findings provide new insights into the polyploidization and paleogenomic evolution of Oleaceae and have important scientific significance for understanding the genetic basis of species and secondary metabolic diversity in Oleaceae.

Eucalypt fossils were widely reported from the Cenozoic deposits across the Southern Hemisphere (Australia, New Zealand, and Argentina). However, no attached reproductive and vegetative fossil remains of this myrtaceous clade have been discovered till now. We report and describe for the first time a fossil eucalypt twig with attached foliage, flower buds, and mature flowers from the early Eocene (~55-52 Ma) sediments (Palana Formation) of Rajasthan, western India. As both vegetative and reproductive organs are in organic connection, they clearly represent the same species. In addition, here we also introduce fossil materials of isolated leaves, flower buds, inflorescence, and flowers recovered from the same stratigraphic level. Our Eocene fossils and extant members of the eucalypt clade are related morphologically by means of robust, thick petiolate lanceolate-shaped leaves with intramarginal secondary veins; operculate flower buds consisting of imbricate petals with discernable margins; solitary inflorescence with three flowers per umbellaster, epigynous and bisexual flowers. Based upon combined characteristics of leaf, flower, and bud morphology, these fossils conform to the Eucalypt clade and are recognized as a new fossil genus and species: Hindeucalyptus eocenicus Patel, R.F. Almeida, Ali et Khan gen. nov. et sp. nov. We also compare it with extant and extinct eucalypts using morphological phylogeny and character mapping analyses. In addition, we briefly discuss its phytogeographic and paleoclimatic implications regarding the distribution and habitat of fossil and modern eucalypts.

The Cucujiformia, with remarkable morphological, ecological, and behavioral diversity, is the most evolutionarily successful group within Coleoptera. However, the phylogenetic relationships among superfamilies within Cucujiformia remain elusive. To address the issues, we conducted a transcriptome-based macro-evolutionary study of this lineage. We sequenced the genomes and transcriptomes of three species from the superfamily Curculionoidea (two from Curculionidae and one from Brentidae), and obtained a data set of more than 569 990 amino acid alignments from 143 species of Cucujiformia. With the most complete collection of whole genomes and transcriptomes so far, we compared the performance of different data matrices with universal-single-copy orthologs (USCO). The resultant trees based on different data sets were consistent for the majority of deep nodes. Two USCO amino acid matrices (i.e., USCO75 and USCO750-abs80) provided well-resolved topology. The analyses confirm that Cucujoidea sensu Robertson et al. 2015 is a nonmonophyletic group, consisting of Erotyloidea, Nitiduloidea, and Cucujoidea sensu Cai et al. 2022. Moreover, Erotyloidea is the early-diverging group, followed by the clade Nitiduloidea. The preferred topologies supported a “basal” split of Coccinelloidea from the remaining superfamilies, and Cleroidea formed the second splitting group. The following phylogeny was supported at the superfamily level in Cucujiformia: (Coccinelloidea, (Cleroidea, ((Lymexyloidea, Tenebrionoidea), (Erotyloidea, (Nitiduloidea, (Cucujoidea, (Chrysomeloidea, Curculionoidea))))))). Our comprehensive analyses recovered well-resolved higher-level phylogenetic relationships within the Cucujiformia, providing a stable framework for comprehending its evolutionary history.

Astragalus (Fabaceae) is astoundingly diverse in temperate, cold arid regions of Earth, positioning this group as a model clade for investigating the distribution of plant diversity in the face of environmental challenges. Here, we identify the spatial distribution of diversity and endemism in Astragalus using species distribution models for 752 species and a phylogenetic tree comprising 847 species. We integrated these to map centers of species richness (SR) and relative phylogenetic diversity (RPD) and used randomization approaches to investigate centers of endemism. We also used clustering methods to identify phylogenetic regionalizations. We then assembled predictor variables of current climate conditions to test environmental factors predicting these phylogenetic diversity results, especially temperature and precipitation seasonality. We find that SR centers are distributed globally at temperate middle latitudes in arid regions, but the Mediterranean Basin is the most important center of RPD. Endemism centers also occur globally, but Iran represents a key endemic area with a concentration of both paleo- and neoendemism. Phylogenetic regionalization recovered an east-west gradient in Eurasia and an amphitropical disjunction across North and South America; American phyloregions are overall most closely related to east and central Asia. SR, RPD, and lineage turnover are driven mostly by precipitation and seasonality, but endemism is driven primarily by diurnal temperature variation. Endemism and regionalization results point to western Asia and especially Iran as a biogeographic gateway between Europe and Asia. RPD and endemism highlight the importance of temperature and drought stress in determining plant diversity and endemism centers.

The two invasive Reynoutria species, Reynoutria japonica var. japonica and Reynoutria sachalinensis, and their hybrid Reynoutria x bohemica are often misidentified by managers and nonspecialists. The taxonomic confusions are all the more exacerbated by the infraspecific variability of introduced populations in terms of morphology, genetic diversity, and ploidy level. We resolved the identity of North-Eastern French invasive populations using 4582 single-nucleotide polymorphisms (SNPs) from a RADseq analysis, DNA contents estimated by flow cytometry, and 12 vegetative morphometric variables. The SNPs supported only one single genotype for R. japonica over 11 localities, while the nine localities of Reynoutria x bohemica were represented by one genotype each. Estimation of genome size using DAPI staining and flow cytometry revealed only octoploid cytotypes for R. japonica and hexaploid cytotypes for R. x bohemica, whereas R. sachalinensis was represented by tetraploid and hexaploid cytotypes. Among morphometric variables, no single one allows for a clear differentiation of the three taxa. We propose a combination of characters to easily and quickly identify these three invasive taxa based on six vegetative criteria including leaf and apex length, as well as leaf shape, leaf base, and apex shape, and the extrafloral nectaries on the node.

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.

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.

The Millettioid/Phaseoloid (or the Millettioid) clade is a major lineage of the subfamily Papilionoideae (Fabaceae) that is poorly understood in terms of its diversification and biogeographic history.To fill this gap,we generated a time-calibrated phylogeny for 749 species representing c.80% of the genera of this clade using nrDNA ITS,plastid matK,and plastome sequence (including 38 newly sequenced plastomes).Using this phylogenetic framework,we explored the clade's temporal diversification and reconstructed its ancestral areas and dispersal events.Our phylogenetic analyses support the monophyly of the Millettioid/Phaseoloid clade and four of its tribal lineages (Abreae,Desmodieae,Indigofereae,and Psoraleeae),while two tribal lineages sensu lato millettioids and phaseoloids are polyphyletic.The fossil-calibrated dating analysis showed a nearly simultaneous divergence between the stem node (c.62 Ma) and the crown node (c.61 Ma) of the Millettioid/Phaseoloid clade in the Paleocene.The biogeographic analysis suggested that the clade originated in Africa and dispersed to Asia,Europe,Australia,and the Americas at different periods in the Cenozoic.We found evidence for shifts in diversification rates across the phylogeny of the Millettioid/Phaseoloid clade throughout the Cenozoic,with a rapid increase in net diversification rates since c.10 Ma.Possible explanations for the present-day species richness and distribution of the Millettioid/Phaseoloid clade include boreotropical migration,frequent intra-and intercontinental long-distance dispersals throughout the Cenozoic,and elevated speciation rates following the Mid-Miocene Climatic Optimum.Together,these results provide novel insights into major diversification patterns of the Millettioid/Phaseoloid clade,setting the stage for future evolutionary research on this important legume clade.

Neuroptera, as a small relic group of Insecta undergoing a rapid species diversification during the Mesozoic Era, is known by diverse extinct endemic lineages preserved as impression fossils and in amber. The current understanding of Mesozoic neuropterans' diversity has mainly focused on the adults, because the contemporaneous larvae have been fairly rare especially for the Jurassic lacewings. Herein, a new giant lacewing larva, Natator giganteus gen. et sp. nov., is described from the Middle Jurassic Daohugou Beds of China. The remarkable larva is characterized by its impressively large body size, distinctively elongated cervix, and presence of swimming hairs on legs, which provide direct evidence to reveal an aquatic habit for the Jurassic lacewing larva. The morphological analysis indicates this giant larva would have probably inhabited the benthic environments of Jurassic montane rivers and streams. In addition, its morphological specialization suggests that it might have adopted an ambush predation strategy to catch its prey. The finding enhances our knowledge of the species diversity and morphological plasticity for the Jurassic lacewing larvae, and reveals that the aquatic lineages of Neuroptera exhibited dramatically structural and ecological convergence across the evolutionary process.

Cotton (Gossypium spp.) is a vital global source of renewable fiber and ranks among the world's most important cash crops. While extensive nuclear genomic data of Gossypium has been explored, the organellar genomic resources of allotetraploid cotton, remain largely untapped at the population level. The plastid genome (plastome) is well suited for studying plant species relationships and diversity due to its nonrecombinant uniparental inheritance. Here, we conducted de novo assembly of 336 Gossypium plastomes, mainly from domesticated cultivars, and generated a pan-plastome level resource for population structure and genetic diversity analyses. The assembled plastomes exhibited a typical quadripartite structure and varied in length from 160 103 to 160 597 bp. At the species level, seven allotetraploid species were resolved into three clades, where Gossypium tomentosum and Gossypium mustelinum formed an early diverging clade rooted by diploids, followed by splitting two sister clades of Gossypium darwinii–Gossypium barbadense and Gossypium hirsutum–Gossypium ekmanianum–Gossypium stephensii. Within the G. hirsutum clade the resolution of cultivated accessions was less polyphyletic with landrace and wild accessions than in G. barbadense suggesting some selection on plastome in the domestication of this adaptable species of cotton. The nucleotide diversity of G. hirsutum was higher than that of G. barbadense. We specifically compared the plastomes of G. hirsutum and G. barbadense to find mutational hotspots within each species as potential molecular markers. These findings contribute a valuable resource for exploring cotton evolution as well as in the breeding of new cotton cultivars and the preservation of wild and cultivated germplasm.

Reynoutria multiflora is a widely used medicinal plant in China. Its medicinal compounds are mainly stilbenes and anthraquinones which possess important pharmacological activities in anti‐aging, anti‐inflammatory and anti‐oxidation, but their biosynthetic pathways are still largely unresolved. Here, we reported a near‐complete genome assembly of R. multiflora consisting of 1.39 Gb with a contig N50 of 122.91 Mb and only one gap left. Genome evolution analysis revealed that two recent bursts of long terminal repeats (LTRs) contributed significantly to the increased genome size of R. multiflora, and numerous large chromosome rearrangements were observed between R. multiflora and Fagopyrum tataricum genomes. Comparative genomics analysis revealed that a recent whole‐genome duplication specific to Polygonaceae led to a significant expansion of gene families associated with disease tolerance and the biosynthesis of stilbenes and anthraquinones in R. multiflora. Combining transcriptomic and metabolomic analyses, we elucidated the molecular mechanisms underlying the dynamic changes in content of medicinal ingredients in R. multiflora roots across different growth years. Additionally, we identified several putative key genes responsible for anthraquinone and stilbene biosynthesis. We identified a stilbene synthase gene PM0G05131 highly expressed in roost, which may exhibit an important role in the accumulation of stilbenes in R. multiflora. These genomic data will expedite the discovery of anthraquinone and stilbenes biosynthesis pathways in medicinal plants.

Species delimitation remains a challenge worldwide, especially in highly diverse tropical and subtropical regions. Here, we use an integrative approach that combines morphology, phylogenomics, and species distribution modeling (SDM) to clarify the cryptic differentiation within the enigmatic hemiparasitic love vine Cassytha filiformis (Lauraceae) in China and adjacent regions. We generated complete plastid genomes and nuclear ribosomal sequences for diverse samples from across the species range and compared results with previously published plastid data, recovering two well-supported monophyletic clades. Further, the analysis revealed significant differences in two morphological characters and SDM, indicating distinct environmental factors influencing their distributions. Fossil-calibrated analyses to estimate the origins and diversification patterns for the cryptic species gave divergence age estimates corresponding to the Oligo-Miocene; a period of new ecological opportunities associated with the prevailing East Asian monsoon. Multivariate analyses support the conclusion that southern China and adjacent regions have a different, previously unknown, cryptic lineage of C. filiformis. Our study highlights the importance of using multivariate approach to characterize plant species, as well as the significant role that past climatic changes have played in driving speciation in parasitic plants in tropical and subtropical zones.

The genus Xylaria comprises a diverse group of fungi with a global distribution and significant ecological importance, known for being a source of bioactive secondary metabolites with antibacterial, antioxidative, anticarcinogenic, and additional properties. In this study, we present a comprehensive taxonomic revision of the species of Xylaria found in some parts of southern China, characterized by an extensive multilocus phylogeny analysis based on internal transcribed spacer (ITS), TUB2 (β-tubulin), and DNA-directed RNA polymerase II subunit 2 (rpb2) gene regions. Morphological examination and detailed comparative analyses of the collected specimens were conducted to determine the distinctiveness of each species. The multilocus phylogeny approach allowed us to infer evolutionary relationships and assess species boundaries accurately, leading to the identification of 40 novel Xylaria species hitherto unknown to science. The newly described species are: X. baoshanensis, X. bawanglingensis, X. botryoidalis, X. dadugangensis, X. doupengshanensis, X. fanglanii, X. glaucae, X. guizhouensis, X. japonica, X. jinghongensis, X. jinshanensis, X. kuankuoshuiensis, X. liboensis, X. negundinis, X. orbiculati, X. ovata, X. pseudoanisopleura, X. pseudocubensis, X. pseudobambusicola, X. pseudoglobosa, X. pseudohemisphaerica, X. pseudohypoxylon, X. puerensis, X. qianensis, X. qiongzhouensis, X. rhombostroma, X. serratifoliae, X. shishangensis, X. shuqunii, X. shuangjiangensis, X. sinensis, X. tongrenensis, X. umbellata, X. xishuiensis, X. yaorenshanensis, X. yinggelingensis, X. yumingii, X. yunnanensis, X. zangmui, and X. zonghuangii. The study's findings shed light on the distinctiveness of the newly described species, supported by both morphological distinctions and phylogenetic relationships with their close relatives. This taxonomic revision significantly contributes to our understanding the diversity of Xylaria in China and enriches the knowledge of fungal biodiversity worldwide.

In this study, we explored the distributions of grass genera in the Southern Cone (SC) of South America, applying several phylogenetic diversity (PD) metrics and randomization tests. Grasses appear to have been present in South America since their early evolution as tropical understory species more than 60 Ma. During the course of evolution, grasses have adapted to all terrestrial biomes and become one of the most successful plant families on earth. At present, the SC contains nearly all terrestrial biomes and a wide range of humid to arid ecoregions. Analyzing 126.514 point occurrences and four plastid markers for 148 genera (91% of the native grass genera), we found that tropical humid regions hold the highest PD, with no observed bias in branch lengths. These results indicate that niche conservatism dominates the diversity pattern of grasses in the SC. We found significantly low PD in the Dry Chaco and in the Patagonian Steppe, which suggest ecological filtering in both warm and cold arid regions. The Patagonian Steppe also holds significantly longer branches than expected by chance, as the native grass flora is mainly composed of distantly related Pooideae genera with a northern hemisphere origin. Short branches are found in the Uruguayan Savanna, suggesting that these grasslands could be a cradle for grass diversity within the SC. The dated phylogeny supported the current view of a relatively recent evolution of the family within the SC, with most diversification taking place from the middle Miocene and onwards.

The Crepidinae are the largest subtribe of the Cichorieae (Asteraceae). Debate remains over the circumscription and phylogeny of this subtribe, mainly due to its complex morphology and the poor phylogenetic signal provided by traditional Sanger sequencing markers. In this study, a well-resolved phylogeny of the subtribe Crepidinae, consisting of seven highly supported clades, was obtained for the first time using nuclear data with a phylogenomics approach (Hyb-Seq). Using this phylogeny along with other evidence, we propose a new taxonomic framework for the Crepidinae with seven lines and 29 genera, which merges subtribe Chondrillinae with the Crepidinae. We also describe a new monotypic genus, Qineryangia, that is characterized by broad involucres, loose imbricate phyllaries with wavy margins, and thick pappus bristles.

As an important halophyte in the Yellow River Delta, the Amaranthaceae C₃ Suaeda salsa (L.) Pall. has attracted much attention for the “red carpet” landscape, and could be simply divided into red and green phenotypes according to the betacyanin content in the fleshy leaves. However, S. salsa has not been sequenced yet, which limited people's understanding of this species at the molecular level. We constructed a high-quality chromosome-scale reference genome by combining high-throughput sequencing, PacBio single molecule real-time sequencing, and Hi-C sequencing techniques with a genome size of 445.10?Mb and contigs N50 of 2.94?Mb. Through the annotation of the S. salsa genome, 298.76?Mb of the repetitive sequences and 23?965 protein-coding genes were identified, of which the proportion of long terminal repeats type in the repetitive sequences was the most abundant, about 50.74% of the S. salsa genome. Comparative genomics indicated that S. salsa underwent a whole-genome duplication event about 146.15 million years ago (Ma), and the estimated divergence time between S. salsa and Suaeda aralocaspica was about 16.9?Ma. A total of four betacyanins including betanidin, celosianin II, amaranthin and 6′-O-malonyl-celosianin II were identified and purified in both phenotypes, while two significantly up-regulated betacyanins (celosianin II and amaranthin) may be the main reason for the red color in red phenotype. In addition, we also performed transcriptomics and metabolomics in both phenotypes to explore the molecular mechanisms of pigment synthesis, and a series of structural genes and transcription factors concerning with betacyanin production were selected in S. salsa.

Jujube (Ziziphus jujuba Mill.), renowned for its nutritional value and health benefits, is believed to have originated in the middle and lower reaches of the Yellow River in China, where it underwent domestication from wild jujube. Nonetheless, the evolutionary trajectory and species differentiation between wild jujube and cultivated jujube still require further elucidation. The chloroplast genome (plastome), characterized by its relatively lower mutation rate compared to the nuclear genome, serves as an excellent model for evolutionary and comparative genomic research. In this study, we analyzed 326 nonredundant plastomes, encompassing 133 jujube cultivars and 193 wild jujube genotypes distributed throughout China. Noteworthy variations in the large single copy region primarily account for the size differences among these plastomes, impacting the evolution from wild jujube to cultivated varieties. Horizontal gene transfer (HGT) unveiled a unique chloroplast-to-nucleus transfer event, with transferred fragments predominantly influencing the evolution of the nuclear genome while leaving the plastome relatively unaffected. Population genetics analysis revealed two distinct evolutionary pathways from wild jujube to cultivated jujube: one driven by natural selection with minimal human interference, and the other resulting from human domestication and cultivation. Molecular dating, based on phylogenetic analysis, supported the likelihood that wild jujube and cultivated jujube fall within the same taxonomic category, Z. jujuba. In summary, our study comprehensively examined jujube plastome structures and HGT events, simultaneously contributing novel insights into the intricate processes that govern the evolution and domestication of jujube species.

Pterocarya (Juglandaceae) is disjunctly distributed in East Asia and the Caucasus region today, but its fossils are widely distributed in the Northern Hemisphere. We first inferred phylogeny with time estimation of Pterocarya under node-dating (ND) based on plastomes of all eight extant species and tip-dating (TD) based on plastomes and 69 morphological characters of 19 extant and extinct species, respectively. We compared the biogeographical reconstructions on the timetrees from ND and TD, respectively, and then compiled 83 fossil records and 599 current occurrences for predicting the potential distributions for the past and the future. The most recent comment ancestor of Pterocarya is inferred in East Asia at 40.46 Ma (95% highest posterior density [HPD]: 28.04–54.86) under TD and 26.81 Ma (95% HPD: 23.03–33.12) under ND. The current distribution was attributed to one dispersal and one vicariant event without fossils, but as many as six dispersal, six vicariant, and 11 local extinction events when considering fossils. Pterocarya migrated between East Asia and North America via the Bering Land Bridge during the early Oligocene and the early Miocene periods. With the closure of Turgai Strait, Pterocarya dispersed between East Asia and Europe through the Miocene. The potential distribution analyses indicated that Pterocarya preferred warm temperate regions across the Northern Hemisphere since the Oligocene, but the drastic temperature decline caused its extinction in high latitudes. Except for Pterocarya fraxinifolia and Pterocarya stenoptera, suitable habitats for this genus are predicted to contract by 2070 due to climate change.

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.