Carya kweichowensis is a critically endangered hickory species endemic to the karst forests of southwestern China. Its survival is threatened by severe habitat fragmentation and extremely small population sizes driven largely by human activities. In this study, we combined population genomic analyses with species distribution modeling to inform the conservation of C. kweichowensis. We sampled 66 individuals from 18 wild populations across its remaining range and generated genome-wide data for single-nucleotide polymorphisms to assess genetic structure, diversity, mutational load, and demographic history. The results revealed clear genetic subdivision of remnant populations into distinct groups corresponding to their geographic isolation. Demographic reconstructions suggested a history of population decline and bottlenecks, emphasizing the prolonged vulnerability of this species. Species distribution models predicted severe contraction and shift of its suitable habitat under future climate change scenarios, which would further imperil its persistence. Based on the genetic differentiation observed, we delineated three conservation units for C. kweichowensis. We recommend immediate conservation action for the marginal central and eastern groups. Our study demonstrates that the integration of population genomics, genetic load assessment, and species distribution modeling contributes profoundly to the development of targeted conservation strategies for endangered species.

Although microbial isolation techniques have been developed for over a century, conventional methods often fail to capture the vast majority of environmental microbial diversity, largely because slow-growing bacteria are outcompeted by fast-growing taxa. To address this limitation, we developed a simple Liquid-Medium-Dilution (LMD) method that physically isolates single cells in liquid microcultures using limiting dilution and the Poisson distribution, without requiring specialized equipment. Comparative analysis of 787 bacterial strains isolated from estuarine sediments of the Qiantang River, China, showed that LMD recovered 72 putative novel species (19.2%), a significantly higher proportion than the Traditional-Solid-Culture (TSC) method (47 strains, 11.4%; P < 0.01). Importantly, LMD uniquely accessed rare and slow-growing lineages, including members of the phylum Verrucomicrobiota and most notably two novel species, Poseidonivirga lenticrescens gen. nov., sp. nov., and Poseidonivirga cretacea sp. nov. These strains exhibit low 16S rRNA gene sequence similarities (90.37% and 90.51%) to known taxa and represent a novel order, Poseidonivirgales, within the class Alphaproteobacteria. Our findings demonstrate that the LMD method effectively minimizes competitive exclusion, enabling the cultivation of previously unculturable, slow-growing, and phylogenetically deep bacterial lineages using standard laboratory conditions.

Gryllidae Laicharting, 1781, the most speciose family within Grylloidea, has a rich fossil record, yet the phylogenetic relationships among these fossil taxa remain poorly resolved. Integration of fossil and extant lineages into a systematic framework has been impeded by sexual dimorphism and the fragmentary preservation typical of compression fossils, thereby confounding homology assessment and topological stability. Here, we describe Elongatitarsus falcatus gen. & sp. nov., represented by a male and a female specimen from mid-Cretaceous Kachin amber, which serves as a morphological bridge linking Cretaceous and extant cricket diversity. To evaluate the phylogenetic signal and homoplasy of different morphological character partitions across fossil and extant Gryllidae, we conducted maximum parsimony analyses using three distinct matrices: a comprehensive morphological matrix, a wing venation-only matrix, and a matrix excluding venation-only fossils. The venation-only matrix yielded poorly resolved topologies with low nodal support; in contrast, the comprehensive morphological matrix recovered a phylogeny partially congruent with recent molecular hypotheses at the subfamilial level, and placed E. falcatus gen. & sp. nov. within Gryllinae. Our results underscore that integrative morphological datasets are essential for reliable placement of fossil taxa. This approach provides a framework for testing the reliability of isolated wings in phylogenetic inferences, offering broader implications for evaluating fragmentary fossil records in deep-time systematics.

Catfishes (order Siluriformes) inhabit diverse aquatic environments worldwide, ranging from tropical lowlands to fast-flowing mountain rivers. However, the contribution of genomic variation to ecological diversification in catfishes, particularly within high-altitude lineages, remains poorly understood. Here, we investigated genome evolution in an extreme environment by focusing on Glyptosternon maculatum, the highest-altitude dwelling catfish known and a basal lineage of Glyptosternoid fishes. We generated a high-quality, haplotype-resolved genome assembly using PacBio HiFi and Hi-C sequencing. The two phased haplotypes span 741.8 Mb and 753.7 Mb, with contig N50 values >4 Mb, representing a substantial improvement in continuity and accuracy over previous assemblies. Comparative genomic analyses revealed significant contraction of gene families associated with G protein–coupled receptor activity, particularly olfactory receptor (OR) and trace amine-associated receptor (TAAR) genes. Water-soluble OR subfamilies exhibited a pronounced reduction relative to other catfishes, suggesting lineage-specific remodeling of chemosensory repertoires that may reflect ecological specialization in high-altitude river systems. Population genetic analyses identified chromosome 11 as the sex chromosome, harboring an ~0.97 Mb sex-determining region (SDR) consistent with an XX/XY system. The X and Y chromosomes are highly similar and lack evolutionary strata, indicating a young, homomorphic pair. Despite limited sequence divergence, the SDR exhibits an enrichment of LINE retrotransposons, with evidence of recent transposable element accumulation extending into adjacent regions. Our results provide a chromosome-level genomic resource for Glyptosternoid fishes and offer new insights into sensory gene evolution and the early dynamics of sex chromosome differentiation in a high-altitude teleost.

Genomes provide the fundamental basis for understanding biological systems. Owing to rapid advances in sequencing technologies and assembly methods, the number of sequenced genomes has increased substantially. A high-quality genome should exhibit high continuity, completeness, and accuracy in its assembly, along with comprehensive and precise annotations of protein-coding genes and other functional genomic elements. However, these standards remain difficult to fully achieve due to technical limitations and inherent genome complexity, especially for plant genomes. This review summarizes current major sequencing technologies and strategies for genome assembly and annotation, elucidates the major challenges encountered in the pursuit of truly high-quality genomes, and provides practical strategies for meeting high-quality genome standards. Finally, we highlight several emerging opportunities and promising research directions across the genomic landscape.

Over the past two decades, advances in high-throughput-sequencing technology platforms and in the recovery of highly degraded DNA have ushered ancient DNA research into the era of deep-time paleogenomics, expanding sample ages from no more than 100 ka to the Early Pleistocene (~ 2 Ma). These developments have resolved long-standing phylogenetic controversies, refined reconstructions of the dispersal and population history across diverse taxa (including humans), and enabled direct investigation of molecular response to Quaternary climate change. Paleogenomic in China developed later than in Europe and North America, with early landmark breakthroughs largely focused on ancient human remains. However, China preserves one of the richest and most distinctive records of Quaternary megafauna, many lineages of which are morphologically and genetically differentiated from their western Eurasian counterparts. Here, we synthesize recent paleogenomic advances across major megafauna clades, including Proboscidea, Perissodactyla, Artiodactyla, and large Carnivora, to evaluate how time-resolved genomic data are reshaping systematics, phylogeography, and evolutionary interpretation of the Chinese Quaternary fauna. Current megafauna paleogenomic coverage remains taxonomically and geographically biased toward northern assemblages and mitochondrial datasets. We therefore outline key methodological and sampling priorities, including coordinated recovery of nuclear genomes and improved approaches for southern contexts with poor preservation, to position Chinese megafaunal paleogenomics as a platform for testing general models of megafauna responses to Quaternary climatic oscillations. These efforts refine the systematics and evolutionary history of Chinese Quaternary megafauna and provide a conceptual model for understanding how megafauna respond to Quaternary climate oscillations worldwide.

Gryllidae Laicharting, 1781, the most speciose family within Grylloidea, has a rich fossil record, yet the phylogenetic relationships among these fossil taxa remain poorly resolved. Integration of fossil and extant lineages into a systematic framework has been impeded by sexual dimorphism and the fragmentary preservation typical of compression fossils, thereby confounding homology assessment and topological stability. Here, we describe Elongatitarsus falcatus gen. & sp. nov., represented by a male and a female specimen from mid-Cretaceous Kachin amber, which serves as a morphological bridge linking Cretaceous and extant cricket diversity. To evaluate the phylogenetic signal and homoplasy of different morphological character partitions across fossil and extant Gryllidae, we conducted maximum parsimony analyses using three distinct matrices: a comprehensive morphological matrix, a wing venation-only matrix, and a matrix excluding venation-only fossils. The venation-only matrix yielded poorly resolved topologies with low nodal support; in contrast, the comprehensive morphological matrix recovered a phylogeny partially congruent with recent molecular hypotheses at the subfamilial level, and placed E. falcatus gen. & sp. nov. within Gryllinae. Our results underscore that integrative morphological datasets are essential for reliable placement of fossil taxa. This approach provides a framework for testing the reliability of isolated wings in phylogenetic inferences, offering broader implications for evaluating fragmentary fossil records in deep-time systematics.

Geothermal systems harbour abundant novel microorganisms, representing substantial phylogenetic and functional diversity among yet-to-be-cultivated bacteria with significant ecological roles. Nevertheless, research on the diversity, metabolic potential, and evolutionary history of these uncultured taxa remains limited. In this study, nineteen metagenome-assembled genomes (MAGs) were recovered from hot springs in Tengchong, Yunnan Province. Phylogenetic analyses indicate that these MAGs form sister lineages to an existing clade, leading to their proposed classification within three novel phyla: Yinglongibacterota, Xuanmingibacterota, and Gonggongibacterota, named after figures from the traditional Chinese legend, Classics of Mountains and Seas. Sequence analysis of both hot spring-derived and published MAGs reveals that all three phyla exhibit similar facultative anaerobic lifestyles. Multiple substrates including cellulose, glucan, pectin, and xylan can be degraded by these phyla, especially Gonggongibacterota, suggesting their critical role in converting complex plant matter into more readily degradable substrates and contributing to sugar fermentation. Furthermore, the ability of these phyla to reduce selenite facilitates environmental detoxification. Notably, gene loss events have resulted in widespread auxotrophy for heme and biotin in these lineages, which may indicate microbial cross-feeding in the community as an adaptation strategy. These pioneering results provide a comprehensive overview of the taxonomic and metabolic characteristics of the three novel phyla, offering insights into their ecological significance and guiding future cultivation efforts.

Endosymbionts are prevalent in insects, establishing close associations with their hosts that range from mutualism to parasitism. Endosymbionts provide hosts with essential nutrients, enhance immunity, and regulate reproduction, thereby profoundly influencing host fitness and adaptive evolution. Such impacts can drive genetic divergence and even speciation over time. Consequently, endosymbionts are critical to understanding the formation of cryptic insect species, which are morphologically indistinguishable yet genetically distinct. Elucidating the mechanisms underlying cryptic speciation remains a central challenge in evolutionary biology, with endosymbionts increasingly recognized as key drivers in this process. In this review, we summarize the fundamental characteristics of insect endosymbionts and their multifaceted roles in host biology. We conceptualize endosymbionts as a critical evolutionary force, focusing on the mechanisms by which they drive cryptic speciation, including ecological adaptation divergence, genetic integration, and reproductive manipulation. By integrating current evidence and elucidating underlying mechanisms, this review presents a framework for understanding endosymbiont-mediated cryptic speciation in insects. Research in this field holds great promise for revealing fundamental evolutionary processes and informing novel strategies for biodiversity conservation and pest management.

Evolutionary relationships of Zanthoxylum L. and Vepris Comm. ex A Juss. remain inadequately resolved due to limited genomic resources and conflicting signals from single markers, hindering efforts to understand their diversification and adaptation across tropical environments. In this study, we generated Angiosperms353 target-capture data for 187 individuals representing 51 Zanthoxylum and Vepris species from East Africa. Using concatenated and multispecies coalescent analyses combined with concordance-factor approaches, we recovered Zanthoxylum and Vepris as monophyletic. However, species-level relationships within each genus exhibited substantial phylogenetic discordance, indicating extensive gene-tree heterogeneity across the dataset. Concordance factor analysis revealed moderate genome-wide site concordance (mean sCF=46.64%) but markedly lower gene concordance (mean gCF=28.77%), indicating widespread gene-tree heterogeneity. Both sCF and gCF exhibited strong positive correlations with branch lengths of r=0.698 and r=0.687, respectively. Discordance patterns showed an almost perfect balance between alternative topologies (sDF1=24.9%, sDF2=24.8%), minimal mean asymmetry (3.5-5.1%), and high proportion of polyphyly (gDFP=59.7%), all consistent with incomplete lineage sorting (ILS) as the primary source of phylogenomic conflict. A small fraction of branches (1.9–4.7%) displayed significant asymmetry, which signals only limited evidence for processes beyond ILS and should be interpreted with caution pending explicit tests of introgression. Generally, our findings offer a comprehensive phylogenomic framework for East African Zanthoxylum and Vepris and demonstrate that ILS has played a major role in shaping genomic variation and phylogenetic discordance within these genera. Further analyses will be required to investigate the extent to which hybridization or other reticulate processes have contributed to their evolutionary history.

Vicariance and dispersal are fundamental biogeographical processes driving the distribution and diversification of species across space and time. This study examines the diversification and origin of some Hydropsyche lineages in the Aegean Archipelago by assessing three biogeographic hypotheses: a vicariance model driven by historical fragmentation, a dispersal model involving colonization across sea barriers, and a mixed model combining both processes. We reconstructed the cladogenesis for species located among island and mainland, estimated divergence times in relation to major paleogeographical events, and examined patterns of island endemism and their distribution. Phylogenetic and time-estimate analyses of mitochondrial cytochrome oxidase subunit I (COI) sequences revealed eight extant lineages exhibiting consistent inter-lineage genetic divergences exceeding 2.5%. These findings suggest a relatively recent diversification history, with primary speciation events during the late Plio-Pleistocene. Widespread species are consistent with a dispersal-driven model because their shallow Pleistocene divergences and large geographical ranges are compatible with recurrent colonization, whereas the geographically restricted island endemics are more consistent with a mixed model (vicariance and dispersal), with confined distributions. Overall, the recovered phylogenetic patterns do not show evidence for an ancient Miocene-vicariance model.

Canavalia gladiata (Jacq.) DC. is a leguminous crop notable for its high protein content and oil rich in unsaturated fatty acids, positioning it as a valuable genetic resource for the diversification and nutritional improvement of legume seeds. Here, we reported a gap-free telomere-to-telomere (T2T) genome assembly of C. gladiata and performed phylogenomic analyses to reconstruct its evolutionary history. Integrative transcriptomic and metabolomic profiling further revealed the transcriptional regulatory networks underlying the biosynthesis of key nutritional metabolites, including amino acids and lipids. These findings lay a foundation for accelerating molecular breeding for improved nutritional quality in C. gladiata. The T2T assembly and multi-omics resources presented herein serve as valuable references for comparative genomics and the genetic improvement of legume crops.

Bulbostylis is the second-most species-rich genus in Abildgaardieae, comprising c. 221 species with a pantropical to warm-temperate distribution and a remarkable ecological and morphological diversity. Despite advances in molecular phylogenetics confirming its monophyly, relationships within Bulbostylis remain poorly resolved, and previous attempts at creating infrageneric classifications are either geographically restricted or unsupported by phylogenetic evidence. Previous molecular studies have sampled fewer than 20% of the species of the genus, limiting our understanding of its evolutionary history. Here, we investigate relationships among 152 species of Bulbostylis, representing 69% of global diversity, using a universal probe kit for targeted genomic sequencing of flowering plants (Angiosperms353 probe kit). Our sampling also includes the genus Nelmesia, which we found to fall within Bulbostylis. We propose a new infrageneric classification and suggest a set of diagnostic morphological characters. Our revised infrageneric classification for Bulbostylis includes 18 sections and 8 subsections, providing a foundation for future taxonomic and evolutionary studies of this ecologically important genus.

Opilioacarida are among the most primitive and enigmatic lineages of mites, retaining numerous plesiomorphic characters that are critical for understanding the early evolution of Parasitiformes. Here, we describe a new extinct family, Plesioacaridae fam. nov., from mid-Cretaceous Kachin amber, representing the second known family within Opilioacarida. The fossil specimen, here named Plesioacarus minutus gen. et sp. nov., was investigated using high-resolution confocal laser scanning microscopy, which revealed an exceptional suite of morphological features clearly distinguishing it from the extant family Opilioacaridae. These include dendritic prodorsal setae, a strongly U-shaped prodorsal furrow, a fused sternapophysis, a pair of setae posterior to the genital plate, a three-clawed palpal apotele, and a three-segmented tarsus I. The morphology of the palp apotele and tarsus I provides new insights into the evolution of appendage segmentation and specialization in early mites. To evaluate its systematic position, we conducted the morphological phylogenetic analysis for Opilioacarida based on 36 discrete characters scored across 22 extinct and extant taxa. The analyses consistently recovered Plesioacaridae as the sister group to all other opilioacarids. This discovery expands the known diversity of Mesozoic Opilioacarida and contributes important evidence for reconstructing the ancestral morphological groundplan and early evolutionary history of Parasitiformes.

Marmota represents a genus of relatively large-bodied, fossorial rodents widely distributed across grassland and alpine meadow ecosystems in the Northern Hemisphere. This study integrates paleontological data with molecular phylogenetics from extant species to reconstruct the spatiotemporal dynamics of Marmota distribution, elucidating its origins, biogeographic dispersal patterns, phylogenetic relationships, and species divergence times. Results indicate that the genus likely originated in North America, with the earliest fossil occurrences dated to ~16.3 million years ago (Mya). The radiation of extant Marmota commenced approximately 6.09 Mya, marked by elevated speciation rates during the Late Miocene and Pliocene. Throughout the late Miocene to the early Pleistocene, the extinction rate was maintained at a relatively stable level. At around 1 Mya, both the speciation rate and the extinction rate increased synchronously, leading to a slight rise in the net diversification rate. These shifts in net diversification rate exhibited strong correlations with global environmental transformations, particularly the expansion of grasslands since the Late Miocene and climatic oscillations associated with the Last Glacial Maximum. Within the context of contemporary anthropogenic climate warming, Marmota species face significant survival challenges, with certain taxa potentially at risk of extinction due to maladaptation to rapidly altering environments.

Spiders exhibit diverse and intricate web-building behaviors, which represent a classic model for studying the evolution of complex traits. Funnel-web architectures occur in several distantly related spider lineages, including Agelenidae and Macrothelidae, suggesting possible convergent evolution of funnel-web-associated traits. This repeated emergence of a complex behavior offers an example of this funnel-web building behavioral convergence. Here, we generated a chromosome-level genome assembly for the agelenid spider Tamgrinia laticeps. Using comparative genomic analyses across 15 spider species with diverse web types, we identified genomic patterns potentially associated with funnel-web-associated behaviors. Numerous genes exhibited convergent shifts in selective pressure, signals of positive selection, or convergent amino acid substitutions. These candidate genes were enriched in functions related to synaptic transmission (e.g., Gabbr1, Crtc1), neural development and neuroregulation (e.g., Rfx2, E(z)), and sensory-motor control (e.g., PKD2, ADORA2A). In addition, convergent amino acid substitutions were detected in several neural and motor-related genes (e.g., VAChT, ine), which exhibited shared substitutions across all three funnel-web building species. This study provides new insights into the genomic basis of behavioral convergence in spiders.

A new genus and species of Marsdenieae, Xua hongheensis, native to the Red River basin of Yunnan Province, China, is described here for the first time and compared with its close relatives. The plant is a perennial, pubescent, twining herb, and is characterized by having small (ca. 1 cm diam.) flowers and fleshy, erect staminal corona lobes with concave apices, and is endemic to the dry-hot valleys of Yimen, Xinping and Yuanjiang Counties, between 1000 and 1200 m, in the Yunnan province of China. In this study, we used plastome data to examine the tribal position of Xua within the family, and seven plastid and nuclear loci to further clarify its phylogenetic relationship. Our family-wide phylogenetic analysis confirms that Xua is a member of Marsdenieae. Our subsequent analyses of Marsdenieae further support that Xua is a distinct genus and probably allied to Dolichopetalum, Cionura, Campestigma, Harmandiella, and Gongronema-Dischidanthus-Sarcolobus. Molecular dating analysis indicates that Xua originated at about 10 Ma and Xua and the five probable allies diverged rapidly over a period shorter than 3 million years, which might be facilitated by both the orogeny and the concurrent reinforcement of East Asian monsoon system during the early Late Miocene. For this new genus and species, a description, illustration, assessment of the conservation status, and its placement in the Marsdenieae phylogenetic tree are provided.

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 region. 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.

Bioluminescence in lampyroid clades represented one of the most distinctive behavioral traits among insects. Although the oldest-known bioluminescent lampyroid clade has recently been reported from the Cretaceous, the diversity and phylogenetic evolutionary history of early bioluminescent lampyroid clades remained unclear. Here, we documented the diversity of early bioluminescent lampyroid clades based on exceptionally well-preserved fossil specimens and further investigated their phylogenetic evolution. Our findings in this study: (1) support multiple independent origins of bioluminescence within the lampyroid clade; (2) present early ecological diversification in the extinct family Cretophengodidae; (3) advance our understanding of biological adaptations in the Cretaceous lampyroid clade; and (4) offer key insights into the evolutionary pathways underlying the origin and diversification of bioluminescence in insects.

Derris trifoliata Lour. is a common mangrove-associated legume important for coastal ecosystem stability and serves as a natural source of rotenoids. However, the lack of high-quality reference genomes has hindered the investigation of its evolutionary history and key functional traits. Here, we present a high-quality, chromosome-level genome assembly for D. trifoliata, representing the first reported genome resource for rotenoid-producing legumes. The assembled genome spans 811 Mb across 11 chromosomes, with a BUSCO completeness of 98.3% and all telomeres and centromeres identified. Evolutionary analysis revealed two rounds of whole-genome duplication event shared with Papilionoideae. The more recent event, along with lineage-specific tandem and proximal duplications, drove the expansion of genes involved in stress responses and secondary metabolism, facilitating adaptation to extreme intertidal environments. Metabolomic profiling identified four major rotenoids predominantly accumulated in roots, which likely provide effective chemical defense against the belowground stress in mangrove habitats. By integrating transcriptomic and metabolomic data, we reconstructed the rotenone biosynthesis pathway and identified candidate enzymes and transcription factors. Notably, the potential tandem expansion and functional evolution of the key biosynthesis genes 2ODDs offer clues to the evolution of specialized biosynthesis pathways. This high-quality genome, combined with multi-omics analyses, provides insight into the environmental adaptation and specialized metabolism of D. trifoliata, establishing a valuable foundation for broader evolutionary research and future biotechnological applications of rotenoid-producing legumes.

We present here a revision of the APG classification that considers the extensive recent analyses of hundreds of nuclear and plastid genes for many angiosperm species. Although previous versions of the APG classification were largely based on uniparentally inherited markers (plastid DNA, largely maternally inherited), there has emerged since APG IV extensive evidence of widespread hybridization and inheritance of ancestral polymorphisms. Despite this evidence of gene-tree discordance, most of the APG IV classification is supported by both plastid and nuclear analyses, and only a few revisions are required in this update to make the classification parallel phylogenetic results in the literature. At the ordinal level, few changes in circumscription are required relative to the last APG version, although the fabids now comprise only the four nitrogen-fixing orders (Cucurbitales, Fabales, Fagales, and Rosales) and the malvids now include the former COM clade (Celastrales, Malpighiales, and Oxalidales), which in nuclear DNA analyses is no longer monophyletic. Oncothecales (with only Oncothecaceae) and Cardiopteridales (with Cardiopteridaceae and Stemonuraceae) are newly recognized, and Icacinales are restricted to Icacinaceae. Restriction of Aquifoliales and Bruniales to just Aquifoliaceae/Helwingiaceae and Bruniaceae, respectively, is also proposed. Huaceae and Columelliaceae are unplaced to order among the malvids and campanulids, respectively. At the family level, expanded circumscriptions include Tecophilaeaceae (including Ixioliriaceae, Asparagales), Frankeniaceae (including Tamaricaceae, Caryophyllales), Phytolaccaceae (including Agdestidaceae and Sarcobataceae, Caryophyllales), Helwingiaceae (including Phyllonomaceae, Aquifoliales), Gesneriaceae (including Calceolariaceae and Peltantheraceae, Lamiales), Pentaphylacaceae (including Sladeniaceae, Ericales), and Orobanchaceae (including Mazaceae, Paulowniaceae, Phrymaceae, and Wightiaceae, Lamiales). In Santalales, the limits of Santalaceae and Olacaceae are revised, and Erythropalaceae and Strombosiaceae are recognized as distinct from Olacaceae; Balanophoraceae are maintained as distinct from Santalaceae, but this is a tentative placement. Generic relationships in Dioscoreales require more analyses before a revised family classification can be proposed, so we maintain the APG IV families of this order.

Co-flowering species in sympatry sharing a common pollinator can mitigate potential reproductive interference through a combination of ethological and mechanical barriers. However, empirical studies integrating both sex-specific foraging and mechanical trait divergence within a specialized pollination system remain rare. To address these questions, the floral rewards, floral visitors, foraging behavior, visitation frequency, pollen-transfer efficiency, and reproductive isolation were compared between two sympatric Lysimachia species: oil-flowered L. congestiflora and nectar-bearing L. stenosepala, which share the oil-collecting bee Macropis omeiensis. Furthermore, we determined the mechanics of spatial partitioning by examining the precise sites of pollen placement and stigma contact on the bee body. In L. congestiflora, female M. omeiensis bees collected floral oil and pollen, and their pollen transfer efficiency (pollen deposition/pollen removal) was higher than that of the other two bee taxa (Halictus spp and Lasioglossum occidens), while in L. stenosepala, both female and male M. omeiensis foraged only for nectar, acting as efficient pollinators. Pollen placement sites on the female oil bee were ventral in L. congestiflora and on the head in L. stenosepala. Male M. omeiensis bees visited the nectar-bearing flower but not the oil flower. Females visited both oil and nectar-bearing species, yet differential pollen placement further reduced interspecific pollen transfer. These results demonstrate that mechanical isolation via spatial pollen placement on shared female bees is the primary mechanism reducing interspecific pollen transfer, while male behavioral specialization provides a complementary barrier. This combination of floral reward divergence and pollinator sex-specific foraging facilitates coexistence of sympatric congeners.

Triplophyllum is a fern genus of about 30 species, distributed across the moist tropical forests of Madagascar, Africa, and the Neotropics. The genus presents significant taxonomic challenges due to a combination of high morphological variability and subtle morphological differences among species. In this study, we use a molecular phylogenetic analysis to identify evolutionary lineages in the Neotropics and assess morphological characters useful for species delimitation. Our sampling encompasses most regions where the genus occurs, and includes three-quarters of the currently recognized species. Our results show that neotropical Triplophyllum species form a single clade, whereas paleotropical species form two clades, and that the circumscriptions of some neotropical species need to be revised. Optimization of morphological characters on the molecular tree reveals extensive homoplasy in indument traits, highlighting the limitations of morphology alone for phylogenetical inferences in the genus. Three new species are supported by both molecular and morphological analyses and are described here in: Triplophyllum atlanticum, T. ctenitoides, and T. dalyi. We also designate a neotype for Triplophyllum funestum, one of the most widespread neotropical species, whose original type has been missing since its description. Because of the intricate evolutionary history of Amazonian biodiversity, traditional morphological taxonomy often fails to appreciate the true species richness of the Amazon and lumps superficially similar lineages into a single species. Our findings reinforce the importance of an integrative approach using molecular and morphological evidence for resolving species delimitation in these cryptic lineages.

DNA methylation is an essential epigenetic mark that involved in a range of biological activities in all domains of life. Molecular mechanisms underlying how the DNA methyltransferases (DNMTs) catalyze cytosine methylation have been well documented in model species. However, it still remains under-investigated on how the functional divergence of different DNMT duplicates have evolved among closely related species. Here, our study addressed evolutionary dynamic, transcriptional regulation and enzyme activities of all the three DNMTs (DNMT1, DNMT2 and DNMT3) in extant Poaceae species. Our results show that, although all Poaceae species are derived from the most recent common ancestor, biased genetic fractionation acting on different DNMT duplicates has resulted in high copy number variations among extant species. In addition, expression-level sub-functionalization (i.e., differential expression genes) is common mechanism that regulates transcriptional pattern of different DNMT duplicates in extant Poaceae species. Neo-functionalization and positive selection further promote functional divergence (i.e., different catalytic efficiency) among different DNMT duplicates. In particular, estimates of enzyme activities demonstrate that highly expressed gene copies of the DNMT1 (i.e., MET1a and MET1b) tend to show high catalytic efficiency. Furthermore, functional analyses of seven DNMT mutants also reveal that loss-of-function of three DNMT genes (OsCMT3a, OsCMT2 and OsDRM2) show complementary impacts on the transcriptional landscape. Our study provides evidence that, while DNA methylation of the three cytosine contexts (CG, CHG and CHH) are all catalyzed by the three DNMTs, different mechanisms have together promoted high evolutionary dynamic and functional divergence in extant Poaceae species.

Selligueoid ferns are arguably one of the only relatively large groups of ferns with uncertain phylogeny, biogeography, and systematics. Previous studies identified some well or moderately supported clades but their relationships were largely unresolved and thus it has been controversial whether these ferns originated from tropical Asia or the Himalaya and how many genera should be recognized. Here we reconstructed phylogenies based on Sanger sequencing data of five plastid markers of 261 accessions representing ca. 103 species and 67 (49 ingroup) plastomes representing 41 species of selligueoids and 18 species of outgroups. Our data resolved selligueoids into six major clades and recovered the monophyly of Arthromeris, Pichisermollodes, and Phymatopteris (excl. type) + Gymnogrammitis, whereas Selliguea will become monophyletic if two isolated species are excluded. Contrasting lumping all genera into one genus, here we propose to recognize six genera: Arthromeris, Phymatopteris, Pichisermollodes, Selliguea, Coumariphylla (4 spp.), and Vietiglossa (1 sp.), in addition to the hybrid genus, × Phymatomeris. We support the proposal to conserve Phymatopteris with a new type. Phymatopteris and Selliguea are found not to co-occur in any locality. Our results suggested that selligueoids originated in the late Eocene (ca. 36.4 Mya) in the Malesia-Pacific area, consistent with the tropical Asian origin hypothesis. Quite surprisingly, only two long-distance dispersals and local range expansions/diversifications contributed to the current distribution pattern of selligueoid ferns. In support of our classification, we provide a key to the six genera, their morphological and geographical synopses, and lists of their constituent species and important synonyms.