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.

Islands are natural laboratories for studying speciation, where geographic isolation can promote rapid diversification. This study investigates the divergence of an insular population of the orchid Epidendrum fulgens on Alcatrazes Island, a land-bridge island off the Brazilian coast. Using an integrative approach, we combined genomic (nuclear and plastid microsatellites), phenotypic (leaf functional traits and floral morphometrics), and ecological (plant community structure and diversity) analyses to test for differentiation from mainland populations. Our results revealed significant genetic divergence, with the island population exhibiting exclusive plastid haplotypes and a distinct genetic cluster, indicating prolonged reproductive isolation despite historical land connections. Phenotypically, insular plants consistently displayed succulent leaves and smaller flowers, traits suggestive of local adaptation to drier conditions and a distinct pollinator regime. Although community-level analyses revealed similar species and phylogenetic diversity, the insular community differed compositionally and exhibited a distinct phylogenetic structure. The confluence of genetic distinctness, adaptive phenotypic traits, and ecological isolation satisfies multiple species criteria, leading us to describe the Alcatrazes population as a new cryptic species. This finding underscores the role of land-bridge islands as engines of speciation, even for species with high dispersal potential, and highlights the critical importance of integrative taxonomy for identifying evolutionarily significant units and informing conservation efforts for insular endemics.

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.

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.

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.