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.

Juglandaceae (the walnut family) comprises nine genera with deep evolutionary history and substantial ecological and economic importance, yet available genomic resources remain fragmented, taxonomically incomplete, and inconsistently annotated. Here, we present Walnut Family DB (WalDB; https://cmb.bnu.edu.cn/WalDB/), a clade-wide multi-omics database specifically developed for evolutionary and comparative genomic research in Juglandaceae. WalDB integrates 79 nuclear genome assemblies, 170 chloroplast genomes, 22 mitochondrial assemblies, population-level variant datasets (SNP and SV VCF files from 10 projects), and transcriptomic resources from six projects and 19 studies. Organized into six interactive modules, the platform enables family-wide exploration of genome structure, gene evolution, and functional divergence. Importantly, to improve cross-species comparability, we generated standardized ab initio annotations for 27 high-quality genomes with unified pipeline, thereby minimizing annotation biases that often hinder comparative analyses across datasets produced by different studies. Integrated tools further support ortholog identification, synteny visualization, co-expression and enrichment analyses, and Ka/Ks-based genomic distances calculation. By combining broad taxonomic coverage with standardized annotation and evolutionary analysis tools, WalDB provides a comprehensive and scalable resource for investigating genome evolution, adaptation, and phylogenetic diversification in Juglandaceae.

Understanding how prokaryotic genomes coordinate nucleotide composition and gene distribution is a central yet unresolved question in genome evolution. Across different genomes, GC-content, nucleotide asymmetries, and biased gene distribution between replication strands are tightly associated, but existing explanations typically address only individual components and lack a unified causal framework. Here, by analyzing 4,012 complete sequences, we show that the variation in GC-content, together with intrinsic constraints imposed by the genetic code and selection, can account for the coordinated evolution of GC-skew, AT-skew and gene strand bias (GS-bias). We show that decreasing GC-content inevitably influences both synonymous codon usage and amino acid usage, thereby enforcing stronger GC- and AT-skews in coding genes and driving a shift between “typical” (GC-skew > 0, AT-skew < 0, and GS-bias > 0 in the leading strand) and “atypical” (GC-skew > 0, AT-skew > 0, and GS-bias > 0) modes of organization. Grounded in first principles, we propose an evolutionary framework that integrates previously proposed hypotheses. This framework explains why atypical organization emerges primarily in low-GC genomes, reveals that mutational biases likely evolved to accommodate the skew requirements of coding genes, and highlights the importance of internal constraints on prokaryotic genome evolution.

Zoogeographical divisions are shaped by species distribution patterns and ecological factors, in which regions delineate areas of faunal similarity and boundaries mark transitions in species composition. However, the zoogeographical division of China has not been assessed using shared-species similarity among multiple basic geographic units and the ecological factors shaping the zoogeographical regions and their boundaries of China remain unclear. Herein, using the multivariate similarity clustering analysis method, we delineated the zoogeographical areas of China based on the distribution data of terrestrial vertebrate species. Then, we assessed the effects of ecological factors on zoogeographical subrealms, regions, and their boundaries by adopting generalized linear models and hierarchical generalized linear models. The results showed that the zoogeographical patterns of China comprised two realms, three subrealms, and eight regions. Contemporary climate, past climate change, vegetation, and terrain influenced the formation of subrealms, while contemporary climate, past climate change, vegetation, terrain, and tectonic movements influenced the formation of regions. Moreover, contemporary climate, past climate change, and tectonic movements shaped intersubrealm boundaries, while contemporary temperature seasonality governed interregion boundaries. Our findings provide a comprehensive quantitative analysis of zoogeographical patterns in China, offer a useful analytical framework for research on biogeographical divisions, and provide insights into the ecological drivers of biogeographical divisions across different spatial scales and biotic groups.

We used reduced-representation genomic sequencing (ddRADseq) to investigate the evolutionary relationships of Myosurus in California. Our phylogenetic analysis reveals a deep divergence between two major subclades, “Longipes” and “Brevipes,” so named because members of the former have scapes generally surpassing the leaves, while those of the latter have shorter scapes (or the flowers and fruiting spikes are ± sessile). Bayesian species delimitation under the multispecies coalescent consistently found ten species in our sample. European M. minimus (represented by one sample) is placed in the “Longipes” subclade but evidently not closely related to the Californian taxa. Also in the “Longipes” subclade, M. filiformis (based on M. minimus var. filiformis) is resolved as sister to a newly discovered lineage, M. “collinus.” Within the “Brevipes” subclade, M. apus (based on M. minimus var. apus) is evidently a rare species restricted to coastal Southern California and northwestern Baja California. Plants previously assigned to M. apus from the Central Valley and Carrizo Plain are resolved in two other newly discovered lineages, M. “vallicola” and M. “digitiformis.” Classification of the plants from Riverside County remains uncertain due to a gap in sampling. Myosurus clavicaulis, first described from southeastern Oregon, is resolved as a distinct species ranging from Northern California and more widely in the Pacific Northwest (east of the Cascade Range). A strong signal of genetic admixture was found in many of our samples, consistent with a model of predominant self-pollination and occasional hybridization as drivers of adaptive divergence.

Phoebe zhennan, an endemic species of Lauraceae in China, is an ecologically and economically important timber tree that has undergone severe population decline and is considered endangered. Despite its importance and threatened status, the absence of haplotype-resolved genomic resources has hindered detailed genetic and evolutionary studies. Here, we report the first haplotype-resolved chromosome-level genome of P. zhennan using ONT ultra-long reads and Hi-C technology. The assemblies for Haplotype A (HapA, 956.20 Mb) and Haplotype B (HapB, 910.89 Mb) were each anchored to 12 chromosomes, with scaffold N50 values of 86.27 Mb and 77.12 Mb, respectively. A total of 33 757 and 33 651 protein-coding genes were identified for HapA and HapB, of which 95% were functionally annotated. Comparative analyses revealed extensive structural heterozygosity, including 112 inversions, 2371 translocations, 6 059 780 single nucleotide polymorphisms (SNPs), 345 228 insertions, and 348 584 deletions. This haplotype-resolved assembly further elucidates the characteristics of chromosomal structural variation and provides an important genetic resource for future studies on the evolution, conservation, and functional biology of P. zhennan.

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.

Sex pheromones are central to mate recognition in moths and often contribute to premating isolation and evolutionary divergence. In moths, female-produced pheromone blends are typically highly species-specific, and even subtle variation in blend composition or component ratios can alter male attraction and reinforce reproductive barriers between closely related species. Recent advances in genomics, functional genetics, and receptor characterization have substantially enhanced our understanding of how pheromone communication systems diverge in sympatric moths through the coevolution of female signals and male perception. Noctuid moths, with their well-documented pheromone production and communication systems, provide an excellent model for studying the evolution of species-specific mate recognition. Here, we review recent advances in the study of pheromone communication in noctuid moths, focusing on three interconnected aspects: pheromone biosynthesis, receptor-mediated recognition, and the evolutionary processes underlying communication divergence. We also assess the extent to which current data support a link between pheromone divergence, male preference, and premating reproductive isolation. Although direct empirical evidence connecting molecular changes to long-term lineage splitting remains limited, noctuid moths provide a powerful comparative system for investigating how chemical communication evolves and contributes to reproductive divergence in insects. More broadly, they offer a tractable model for understanding how signal-receiver coevolution, and gene-family evolution interact during premating isolation and lineage divergence in chemical communication animals.

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.

Many bird species with broad geographic distributions exhibit complex patterns of lineage divergence shaped by historical isolation, migration, and gene flow. The American robin, Turdus migratorius, is found throughout North America and includes seven described subspecies that differ in plumage and migratory behavior, yet their evolutionary relationships remain uncertain. Here, we used genome-wide SNP data, population structure analyses, phylogenomic inference, divergence time estimation, and D-statistics to reconstruct relationships within the T. migratorius complex and evaluate patterns of lineage divergence and introgression. Our analyses consistently recovered four principal genomic lineages that do not correspond to currently recognized subspecies: (1) T. m. confinis from Baja California Sur, (2) a Mexican lineage, (3) western North America, and (4) boreal eastern North America. Time-calibrated analyses indicate a deep late-Miocene divergence (~8 Ma) separating T. m. confinis from all other lineages, followed by Pleistocene diversification among the remaining groups. Genome-wide differentiation and long-term isolation support the recognition of T. m. confinis as an independently evolving lineage consistent with species-level status. In contrast, Turdus rufitorques, which is traditionally considered the sister species of T. migratorius, was nested within the Mexican lineage. Significant D-statistics revealed excess allele sharing between the Mexican lineage and T. rufitorques, supporting a history of introgression. This study refines species limits within the American robin complex and highlights the importance of genome-wide data for resolving evolutionary independence in widespread migratory birds.