The evolutionary arms race between insects and their predators has fueled remarkable defensive adaptations, offering insights into ecological dynamics across deep time. Fossils provide critical evidence for studying the evolution of defense strategies. Here, we describe a new lineage of Clambidae from mid-Cretaceous Kachin amber, Scutacalyptus kolibaci gen. et sp. nov. Scutacalyptus stands out within the family due to the flattened body and fully explanate body margins. The diversity of defensive morphotypes in Cretaceous Clambidae, including conglobators like Sphaerothorax, semi-flattened forms like Acalyptomerus, and shield-formers like Scutacalyptus, highlights their developmental plasticity and suggests ecological differentiation in response to varied predation pressures during the late Mesozoic. This morphological divergence reflects niche partitioning in the Cretaceous forest floor ecosystem, driven by a diverse predator array including spiders, ants, lizards, and birds. The coexistence of clambids with spines or explanate margins parallels adaptations in the modern, unrelated Cassidinae, where tortoise beetles use explanate margins and some leaf-mining beetles use spines, each tailored to counter specific predation pressures. These parallel strategies reveal how different defenses likely addressed distinct ecological challenges in the mid-Cretaceous.

Oxidative stress, triggered by hypoxia during repetitive diving, represents a notable environmental adaptation of marine mammals. Glutathione (GSH) is a widely acknowledged antioxidant that protects crucial cellular elements from damage by reactive oxygen species (ROS). Nevertheless, the role of the glutathione metabolism pathway in shaping the adaptation to oxidative stress in marine mammals is not fully elucidated. In this study, we conducted evolutionary analyses on 37 genes related to GSH metabolism pathway in marine and terrestrial mammals. We found that in comparison with their terrestrial relatives, marine mammals showed convergently accelerated evolution on the core modules of GSH metabolism. Specifically, we identified a total of 16 genes with significant evolution signals unique to marine mammals, and several genes (e.g., accelerated evolution genes: RRM1 and SMS, positively selected genes: ANPEP and GCLC) were shared in marine mammal lineages. Eight genes were discovered to possess specific amino acid modifications that are common among all marine mammals. Functional assays of marine mammal GCLC showed a downregulation of HIF-1α and enhanced GSH levels under hypoxic conditions, suggesting heightened protection of marine mammals against oxidative stress induced by hypoxia. Our study identified key genes with significant evolutionary signals in marine mammals, providing genomic and functional support for convergent hypoxia adaptation mechanisms within this taxon.

Weasels represent the most widely distributed and diverse lineage within the family Mustelidae. They have experienced adaptive radiation and have long been the subject of significant taxonomic debates. This study undertakes a comprehensive study of this group, employing morphological measurements, mitochondrial genomes, nuclear genes, and single copy orthologs extracted from whole genome data. Based on the outcomes of phylogenetic tree construction using orthologous genes, it is ultimately verified that the genera Mustela and Neogale are independent genera, thereby resolving the controversy regarding the species they encompass. Through molecular systematics and morphological studies, a putative Mustela species collected from Mabian Dafengding Nature Reserve in Sichuan is confirmed as a new species, designated Mustela mopbie sp. nov. This new species exhibits molecular phylogenetic affinity with M. altaica and M. nivalis, yet shares morphological similarities with M. kathiah, M. nivalis and M. aistoodonnivalis. Notably, it is considerably smaller than these species and possesses distinctive body coloration and tail morphology. This study provides a detailed description of this new species and demonstrates that larger datasets yield more robust phylogenetic signal. Furthermore, we observed substantial incongruence between mitochondrial and nuclear gene trees, suggesting potential genomic introgression between this new species and its closely related congeners (M. altaica and M. nivalis).

Sex ratio plays a critical role in population survival. Dioecious plants may simultaneously display sexual dimorphism and deviations from the equilibrium expectation of 1:1 sex ratio in populations, i.e., biased sex ratio. However, whether biased sex ratios can be attributed to sexual dimorphism has not been well investigated. Here, we conducted experiments using a three-water depth gradient to examine sexual dimorphism performance and population sex ratios for Vallisneria natans, and investigated the variations of natural population sex ratios for it and other two congeners V. spinulosa and V. densesenulata along water depth changes. Females of V. natans had higher reproductive investment than males, and the degree of sexual dimorphism increased with increasing water depth. At greater water depths, increased reproductive expenditure led to higher mortality in females, resulting in a male-biased sex ratio. The sex ratios of natural V. natans and V. spinulosa populations did not significantly deviate from 1:1. In contrast, populations of V. densesenulata exhibited markedly a female-biased sex ratio, which may be attributed to female plants producing more clonal ramets. Furthermore, no evidence was found for variation in sex ratios along water depth gradients in natural populations of any of the three species. These findings highlight the plasticity both of sexual dimorphism and sex ratios in dioecious plants, indicating that sex ratios are species-specific and depend on sex-specific life-history strategy shaped by their growth environments.

Understanding the genetic diversity and genetic load of endangered species is essential for developing effective conservation strategies, particularly in ecologically sensitive regions such as the Himalayas. Cupressus austrotibetica, a rare conifer and the tallest recorded tree in Asia, reaching up to 101.2 m, faces substantial anthropogenic and environmental threats. To evaluate its genetic status, we sequenced transcriptomes of 54 individuals sampled across its restricted range and compared them with 96 individuals of C. gigantea, a closely related endangered species with broader distribution at higher elevations. Our analysis reveals that C. austrotibetica exhibits higher genetic diversity (π = 0.0091) compared to C. gigantea (π = 0.0042). Demographic analyses identified three historical bottleneck events in C. austrotibetica and two in C. gigantea, with two of these events coinciding with Quaternary climatic oscillations. Despite its relatively high genetic diversity, C. austrotibetica has a smaller effective population size based on Stairway Plot 2 (Nₑ ≈ 7200) than C. gigantea (Nₑ ≈ 17 600). Furthermore, C. austrotibetica harbors a higher proportion of severe deleterious mutations, while C. gigantea retains more moderate deleterious variants. These findings indicate that a recent anthropogenic bottleneck event has likely driven the reduced population size and increased genetic load in C. austrotibetica, emphasizing the urgent need for conservation priorities for this imperiled species.

The genus Magnolia belongs to Magnoliaceae, an early diverging lineage of the Magnoliales, and is cultivated globally for its high ornamental and commercial values. Meanwhile, as the large genus in the family Magnoliaceae, Magnolia species are regarded as highly value in phylogenetic and conservation biological studies. However, the whole genome data of Magnolia is still relatively insufficient in previous research. Here, we present a high-quality, chromosome-level genome sequence of Magnolia sinostellata (1.86 Gb) with a scaffold N50 of 85.33 Mb. The nineteen M. sinostellata genome chromosomes revealed eleven main duplications representing subgenome. Comparative genomics analysis elucidates that the variance in the number of abiotic stress resistance genes among Magnoliids species are related to different environmental adaptations. Most of the genes related to MAPK signaling and stress resistance pathways in the investigated M. sinostellata species are expanded as compared to the other species. Furthermore, the comparative genomics analysis of three Magnolia assemblies, M. sinostellata, M. biondii, and M. sieboldii reveal that large inversions enriched in terpenoid metabolic pathways, stress resistance and flavonoid biosynthesis, and DNA replication proteins. Using transcriptome sequencing data, we analyzed the expression levels of genes related to terpenoids biosynthesis (terpene synthase, TPSs) and ICE-CBF-COR gene models related to cold tolerance in various tissues and the buds under different temperature conditions. The high-quality assembly of M. sinostellata and ICE-CBF-COR bioinformatic analysis cascade provide valuable resources for studying the phylogenetic and evolution of Magnoliaceae and angiosperm, while the candidate genes will provide foundational support for molecular breeding in Magnolia species.

The peppered moth Biston betularia L., widely distributed across the Northern Hemisphere, represents an ideal organism for exploring phylogeographic pattern and evolutionary history. In this study, we integrated molecular, morphological, and distributional data of this species to reconstruct its phylogenetic relationships, estimate divergence times, infer the geographic origin, and trace dispersal routes. Molecular analyses identified six monophyletic lineages (HM, NC, HD, E, NA I, and NA II). With the exception of the sympatric North American lineages NA I and NA II, the remaining lineages exhibit allopatric distributions across Eurasia. Ancestral area reconstruction and approximate Bayesian computation (ABC) analyses supported a southern Xizang origin within the Himalayan Mountains, consistent with the ‘Xizang-origin hypothesis’. The colonization of North America occurred twice via the Bering Land Bridge during the Pleistocene glaciation. Collectively, the current genetic pattern is best explained by gradual allopatric differentiation following long-distance dispersal and subsequent isolation. Furthermore, we reconstructed the global dispersal history of B. betularia. These results indicated that in situ speciation within the Himalaya may be more common than previously recognized, challenging the notion that Himalayan fauna are predominantly considered ‘immigrant’. This study enhances our understanding of Himalayan zoogeography and biodiversity through the resolved evolutionary history of a widely distributed species.

Accurate species delimitation is crucial for biodiversity research, as it significantly impacts taxonomy, ecology, and conservation. Recent advances in molecular phylogenetics and integrative taxonomy have improved classifications and resolved long-standing taxonomic uncertainties. Here we use Hyb-Seq (489 nuclear loci) and phylogenomic approaches to investigate Afrocarduus, a genus endemic to tropical Afromontane and Afroalpine regions. Our analyses reveal 16 evolutionary lineages within this relatively young genus (crown age 2.3 Mya), with new morphological data strongly supporting the recognition of each lineage as a distinct species. We demonstrate that the stemless habit evolved independently in species from the Ethiopian Highlands and the East African Rift System (EARS). Notably, we show that the concept of the stemless A. schimperi adopted by the Flora of Tropical East Africa, in fact, comprises seven clearly recognizable species, which we formally reinstate. Unexpectedly, the stemmed A. nyassanus was recovered as paraphyletic with A. ruwenzoriensis nested within it, probably due to incomplete lineage sorting or hybridization. Additionally, the stemmed A. keniensis may represent a complex of cryptic species, and we describe a new stemmed species from southern Ethiopia, A. kazmi sp. nov. We expand the number of accepted species in Afrocarduus from eight, as recognized in the Flora of Tropical East Africa, to 18 (including two species for which we were not able to obtain molecular data). Our study thus highlights a substantial prior underestimation of the diversity of Afrocarduus in Afromontane and Afroalpine habitats.

Identification of Fabaceae family Plants, traditionally relies on either morphological traits or DNA barcoding, each with limitations in accuracy and efficiency. Deep learning has emerged as a promising tool for integrating multiple data sources, but its full potential remains underexplored. This study aimed to utilize a deep learning model that integrates morphological and molecular data for species identification within Fabaceae family, bridging the gap between the two methods of identification. The research involved four main phases: (i) data collection, (ii) data preprocessing, (iii) training and testing the model, and (iv) results analysis. The data comprised DNA barcode sequences retrieved from the BOLD database, and images were collected from different websites. The model was trained for identification on the genera and species level, with two different barcodes, ITS2 and matK+rbcL. Only species with four available copies of ITS2, matK, and rbcL sequences were selected to ensure consistent input across samples.  The final dataset included 7 genera and 21 species. While the model achieved high accuracy during training, test accuracy remained low (14–19%), indicating overfitting, likely due to the limited dataset size. However, the model demonstrated the ability to evaluate barcode discrimination across genera. Specifically, it highlighted ITS2 and matK+rbcL as having varying levels of effectiveness depending on the genus. These findings introduce a new application for deep learning in plant systematics not only for species identification but also for evaluating barcodes. This approach could help reduce the reliance on trial-and-error in barcode selection and enhance the efficiency of molecular taxonomy. 

The genus Kineococcus is primarily found in extreme environments and plant-associated habitats, suggesting its potential for stress tolerance and plant growth promotion. However, the diversity and functional potential of this genus remain largely unexplored, mainly due to the limited availability of strains and genomic resources. In this study, 33 Kineococcus strains were isolated from the Gurbantunggut Desert and Shanshan Kumtag Desert in Xinjiang, China. Based on the overall genome relatedness indices (OGRI) and sampling origins, 12 representative Kineococcus strains were selected for polyphasic taxonomy and assessment of plant growth promoting traits. By integrating phylogenetic, morphological, physiological, chemotaxonomic, and genomic analyses, these strains were classified into nine novel species (one with two subspecies). The representative isolates exhibited various key plant growth-promoting traits, including siderophore production, cellulose degradation, organophosphate solubilization, and indole-3-acetic acid (IAA) production. This study significantly expands the strains, species, and genome resources of the genus Kineococcus, providing valuable insights into its ecological adaptation, particularly in saline-alkali tolerance, and growth-promoting potential for sustainable agriculture.

A new species, Sinocurvicubitus haotianus Xu, Shih, Ren et Wang, sp. nov. (Curvicubitidae), is described from the Upper Permian Leping Formation in Jiangxi Province, South China. This constitutes the second definitive occurrence of Curvicubitidae in the Late Permian. Through comparative wing morphology and cladistic analyses, we resolve phylogenetic relationships within the superfamily as ((Ignotalidae + Pereboriidae^*) + Curvicubitidae) and validate the exclusion of Scytophara extensa from Pereboriidae. Additionally, we estimate divergence times across Pereborioidea lineages, reconstruct ancestral distribution ranges, and elucidate the origin centers and dispersal routes for Curvicubitidae. Wing eyespots and bands suggest predator mimicry, a novel defense strategy in Permian insects.

Carpesium (Asteraceae) represents the largest Asian genus within the subtribe Inulinae of the tribe Inuleae, exhibiting maximum species diversity in China. This study presents the first comprehensive phylogenetic analysis of Carpesium, utilizing nuclear ribosomal ITS, specific chloroplast DNA sequences (rps16-trnQ, rpl32-trnL and ndhF-rpl32), whole chloroplast genomes and chloroplast coding sequence (CDS). The results demonstrate that Carpesium, excluding C. abrotanoides, constitutes a monophyletic group. The Carpesium s.str. clade contains two well-supported lineages with distinct morphological characteristics. Based on morphological analyses, molecular phylogenetic evidence, and karyotypic studies, this research establishes Cladocarpesium gen. nov. to accommodate Carpesium abrotanoides. The comprehensive sampling approach has facilitated a thorough phylogenetic reconstruction of the Inula complex, establishing a robust systematic framework that clarifies previously uncertain relationships among constituent species. This multilocus methodology provides essential insights for reassessing infrageneric classifications within this taxonomically complex group.