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 chromosomes frequently undergo turnover through the recruitment of new sex-determining genes or translocation of ancestral genes. This phenomenon is particularly evident in Salix (Salicaceae). In Populus, the sister genus of Salix, a partial-ARR17-based sex-determination mechanism has been reported, and is also found in several Salix species. In Vetrix 15ZW clade I of Salix, species share a female heterogamety system on chromosome 15. A partial-PI (PISTILLATA)-based mechanism has been proposed for several species in this clade, exceptS. purpurea, which appears to employ a two-gene model involving ARR17 and GATA15. To further investigate the evolution of sex-determining factors in this clade, we assembled a high-quality, haplotype-resolved genome of S. integra, a close relative ofS. purpurea. Based on resequencing data from males and females, we identified W- and Z-linked regions located in pericentromeric regions on chromosome 15, consistent with those reported in other Salix species. Comparative analyses showed that S. integra possesses a partial-PI-based mechanism, supporting the hypothesis that PI sequences were recruited in the ancestor of 15ZW clade I, whereas the ancestor ofS. purpurea recruited a two-gene model later. Together, these results advance our understanding of the relationship between sex-determining plasticity and sex chromosome evolution in plants.

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.

Nymphaeales, an early-diverging angiosperm order, is pivotal for understanding floral evolution, yet the processes of floral organogenesis and the evolutionary transitions between Cabombaceae and Nymphaeaceae remain incompletely resolved. Here, we integrate scanning electron microscopy, phylogeny-based ancestral state reconstruction, and comparative genomics to investigate floral organogenesis and MADS-box gene families in Brasenia schreberi (Cabombaceae) and Euryale ferox (Nymphaeaceae). Brasenia schreberi exhibits a stable trimerous, whorled initiation pattern; its floral apex remains dome-shaped and produces a superior gynoecium with free (apocarpous) carpels. In contrast, E. ferox displays a tetramerous pattern with unidirectional (abaxial-to-adaxial) initiation followed by spiral centripetal organ formation; its apex becomes concave early, forming a complex receptacle that develops into an inferior gynoecium with syncarpous carpels. Ancestral state reconstructions indicate that Cabombaceae retains more plesiomorphic traits of the Nymphaeales ancestor, whereas Nymphaeaceae exhibits multiple derived innovations. Using a domain- validated, de-redundant dataset, we further compare MADS-box phylogeny and motif architectures, revealing relatively conserved motifs in ABCDE-related MIKC clades but more heterogeneous patterns in certain non-ABCDE lineages, partly influenced by annotation quality. Together, these results support independent evolutionary trajectories for Cabombaceae and Nymphaeaceae and shed light on the evolution of floral organization in basal angiosperms.

Orchidantha, the sole genus in the family Lowiaceae (Zingiberales), exhibits distinctive, orchid-like flowers that emit a carrion-like scent, attracting dung beetles for pollination. Despite their ecological and ornamental value, many Orchidantha species are endangered and face an elevated risk of extinction. Here, we present the first chromosome-scale genome assembly of the endangered Orchidantha insularis from Hainan Island. The 2.24 Gb genome was assembled into nine pseudochromosomes, and 31,541 protein-coding genes were annotated. Phylogenomic analysis places O. insularis within the 'banana group' of Zingiberales and indicates divergence from Musaceae approximately 65 Ma, following a shared recent whole-genome duplication (WGD). We identify significant expansions in gene families related to photosynthesis and carbon fixation, consistent with adaptation to low-light tropical understory habitats. Our analysis uncovers the genetic basis of the carrion-like floral scent in O. insularis by revealing complete biosynthetic pathways for dimethyl disulfide (DMDS) and indole. In parallel, the expansions of FMO genes and signatures of positive selection reinforce indole metabolism, which links floral scent production to both adaptation and defense. Whole-genome resequencing of population samples revealed high genetic differentiation and low nucleotide diversity. Demographic inference indicates severe Pleistocene bottlenecks followed by continued population decline. Together, these results provide a genomic foundation for understanding genome evolution in early-diverging Zingiberales and inform conservation and horticultural use.

The Eurasian and North African Asparagaceae subtribe Hyacinthinae Parl. comprises 15-21 genera of mostly spring-flowering bulbs with great diversity in the Mediterranean. Many genera are horticulturally important, notably hyacinths, grape hyacinths, and squills. Understanding of relationships among these genera remains limited with widely differing classifications in use and scattered phylogenetic sampling. A comprehensive morphological investigation of the Hyacinthinae increased the number of recognized genera from nine to 21, based largely on bulb characteristics. However, this treatment has not been widely adopted despite some support from later molecular analyses. This case study on the generic limits of a horticulturally important plant group raises key issues of gaining user acceptance of a nomenclatural system where some familiar genera are substantially redefined. To date there has not been a detailed combined molecular and morphological study of the subtribe. We reconstructed the most comprehensively sampled phylogeny of Hyacinthinae to date, using 246 low-copy nuclear genes from Angiosperms353 and plastome sequences. Morphological data were compiled from published literature, and direct observations. Our nuclear and plastid phylogenies of Hyacinthinae recover 18 of 21 possible genera while the remaining three are para- or polyphyletic. However, relationships among the genera vary between datasets. Quartet scores indicate incomplete lineage sorting or hybridization, especially those where there is cytonuclear discordance. Our data provide strong support for the transfer of two species of Hyacinthus to Fessia, illustrating the problems arising from convergent floral traits. This paper offers a major step forward in the delimitation of Hyacinthinae genera.

Robust phylogenies and comprehensive taxonomies are fundamental for understanding the evolution and classification of species-rich genera. Corydalis (Papaveraceae), comprising approximately 530 species, is one of the largest and most diverse angiosperm genera. While a recent classification system has been established based on phylogenomic and morphological evidence, it relied primarily on plastid genomic data, with limited consideration given to nuclear genes. Here, we compiled the genome skimming data from 411 accessions representing 265 species covering all recognized 39 sections of Corydalis. Using 6617 high quality nuclear single nucleotide polymorphisms (SNPs) and eight single-copy nuclear genes (SCNs), we reconstructed a comprehensive phylogenetic framework for Corydalis. Our results strongly supported the division of Corydalis into four subgenera, including subg. Cremnocapnos, subg. Bipapillatae, subg. Sophorocapnos, and subg. Corydalis. Of the 33 sections sampled with multiple species, ten were recovered as non-monophyletic, including sect. Cheilanthifoliae, sect. Thalictrifoliae, sect. Vermiculares, sect. Rupifragae, sect. Asterostigmata, sect. Mucronatae, sect. Elatae, sect. Fasciculatae, sect. Flexuosae, and sect. Bimaculatae. Phylogenetic network analyses revealed pervasive hybridization and introgression in subg. Corydalis, suggesting that widespread hybridization and introgression are major drivers of both phylogenetic discordance and sectional non-monophyly. Our study not only provides a critical nuclear genomic perspective for Corydalis, but also offers concrete guidance for refining its infrageneric classification. In addition, our findings also underscore the necessity of future studies that integrate expanded sampling, high-quality genetic markers, and morphological data to resolve the classification of taxonomically problematic sections.

Dalbergia (Leguminosae) is a pantropical genus that serves as an ideal system for studying pantropical biogeography and diversification. However, limited taxon sampling and molecular data have hindered the resolution of intrageneric relationships and understanding of its evolutionary history. Here, we reconstruct a densely sampled phylogeny of Dalbergia based on hybrid capture of 89 low-copy nuclear loci, including 98 species spanning all major biogeographic regions and most previously recognized taxonomical clades. Phylogenetic analyses using concatenated and coalescent approaches support the monophyly of Dalbergia and consistently identify six major clades, including a distinct and newly identified Africa-Madagascar lineage (clade E) with potential taxonomic significance. Our results propose merging two of its sections, sect. Dalbergia and sect. Selenolobium, and expanding sect. Ecastaphyllum to include some African species. Topological incongruences observed between concatenated and coalescent trees, together with the high gene tree conflict at certain nodes, are consistent with localized effects of hybridization and/or incomplete lineage sorting. Divergence dating and model-based biogeographic analyses support a Neotropical origin of Dalbergia in the middle Eocene (~39 Ma), followed by repeated long-distance dispersal events from Africa to Asia, Neotropics, and Madagascar, and back into the Neotropics. An early diversification burst in Africa during the late Oligocene–early Miocene (~27–18 Ma) preceded the genus’s intercontinental expansion. Diversification rates are high across all four regions, with Madagascar showing the highest speciation rate. These macroevolutionary dynamics coincided with Eocene–Miocene climatic changes and habit shifts. This study provides a robust phylogenetic framework for Dalbergia, refines its temporal and biogeographic history, and illustrate how dispersal, climatic change, and lineage-specific diversification have interacted to generate pantropical biodiversity.

Singing is a key innovation that drives the diversification of crickets. However, acoustic-related traits have not been investigated in a broad phylogenetic context, making the evolution of acoustic communication enigmatic. To explore the evolution and regression of singing and hearing, we examined over 100 species of tree crickets (Oecanthidae), a family with diverse acoustic-related traits that has never been considered in an evolutionary context. We investigated homologous traits related to sound production (stridulatory file, harp, and mirror) and reception (tympana, inner, and outer). Using a robust, time-calibrated molecular phylogeny, we estimated ancestral states and evolutionary rates and tested for correlated evolution. We quantified the phylogenetic signal for each trait to assess how evolutionary relatedness predicted acoustic trait similarity. Our analyses revealed multiple independent losses of sound-producing structures in the forewings and hearing organs, providing evidence for the convergent evolution of the silent phenotype. Our results also suggest a high level of integration among wing veins, particularly those related to acoustic communication. We discuss the potential ecological drivers of these patterns, such as predator avoidance and habitat shifts, and substantiate how alternative phenotypes, like “silent listeners” and “deaf singers”, facilitate evolutionary transitions between acoustic and vibratory signaling (biotremology). Our findings provide a model for understanding the macroevolutionary dynamics of sensory regression, a pattern shared across diverse animal systems. The evolutionary trends in the acoustic signaling of Oecanthidae provide a powerful system for studying the macroevolutionary dynamics of communication.