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 (N_e ≈ 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.

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 the 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.

The genus Magnolia belongs to Magnoliaceae, an early diverging lineage of the Magnoliales, and is cultivated globally for its high ornamental and commercial values. As a large genus in the family Magnoliaceae, Magnolia species are regarded as highly valuable in phylogenetic and conservation biological studies. However, the whole genome data of Magnolia is still relatively insufficient. 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 19 M. sinostellata genome chromosomes revealed 11 main duplications representing the subgenome. Comparative genomics analysis revealed that the variance in the number of abiotic stress resistance genes among Magnoliid 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, compared to the other species. Furthermore, the comparative genomics analysis of three Magnolia assemblies, M. sinostellata, Magnolia biondii, and Magnolia sieboldii revealed that large inversions were 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 terpenoid biosynthesis (terpene synthase) 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 the ICE–CBF–COR bioinformatic analysis cascade provide valuable resources for studying the phylogeny and evolution of Magnoliaceae and angiosperms, while the candidate genes will provide foundational support for molecular breeding in Magnolia species.

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, that is, 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 in natural population sex ratios for it and two other congeners V. spinulosa and V. denseserrulata 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. denseserrulata 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.

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 National 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).

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 internal transcribed spacer (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 C. 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.

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 the 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) analysis of results. 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 levels, 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 data set included seven 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 data set 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.

Chimonocalamus is distinguished by pachymorph rhizome, lower culm nodes with a ring of root thorns, and semelauctant inflorescence. However, species identification in this genus can be confused due to similar morphological features and overlapped geographical distribution. To confirm the identities of Chimonocalamus species in China, plastome and nuclear ribosomal (nrDNA) of 49 accessions of 10 known species and three putative new species were newly retrieved by genome skimming. Distance-based and tree-based methods were conducted to analyze the species discrimination rate of six datasets. The Skmer method was also applied. The results indicated that Skmer analyses had the highest discriminatory power with nine species identified (69.23%). The plastome showed much higher discriminatory success rate than the combination of three standard plastid DNA barcodes, which performed worst among the six datasets. The three potentially new species of Chimonocalamus were confirmed by the plastome and nrDNA datasets, and Skmer analysis, together with morphological differences. Herein, we describe and illustrate the three species as new to science, that is, Chimonocalamus hekouensis Y. X. Zhang, Gui L. Zhang & D. Z. Li, Chimonocalamus hsuehiorum D. Z. Li & Y. X. Zhang, and Chimonocalamus shuangjiangensis D. Z. Li & Y. X. Zhang. Moreover, the Chimonocalamus fimbriatus complex was designated, calling for further investigation. Taken together, plastome and nrDNA could serve as effective super-barcodes for species discrimination of Chimonocalamus, playing important roles in recognition of cryptic new species, and Skmer analysis can be adopted in molecular identification. Our study provides an empirical case for molecular discrimination of bamboos and can be meaningful for other plant groups.

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 insight into its ecological adaptation, particularly in saline–alkali tolerance, and growth-promoting potential for sustainable agriculture.

A new species, Sinocurvicubitus haotianus Xu, Shih, Ren & 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 resolved phylogenetic relationships within the superfamily as ((Ignotalidae + Pereboriidae*) + Curvicubitidae) and validated the exclusion of Scytophara extensa from Pereboriidae. Additionally, we estimated divergence times across Pereborioidea lineages, reconstructed ancestral distribution ranges, and elucidated the origin centers and dispersal routes for Curvicubitidae. Wing eyespots and bands suggested predator mimicry, a novel defense strategy in Permian insects.

Meiogyne is a genus of shrubs, trees and treelets occurring in India, tropical Southeast Asia, and Australasia–Pacific, an unusually wide distribution across Australasia and the Western Pacific compared to other genera of Annonaceae. Previous chloroplast phylogenies of the genus offered poor resolution and support. Here, a molecular phylogeny was reconstructed based on 27 described Meiogyne species (ca. 70% sampling) using seven chloroplast and 11 nuclear markers. The combined data set generated a well-resolved and well-supported phylogeny. Estimation of divergence time utilized two fossil calibrations and an uncorrelated log-normal relaxed clock model. Trait-dependent and trait-independent biogeographical models in BioGeoBEARS were compared using corrected Akaike information criterion weight and the likelihood ratio test. The results suggest that narrow monocarp width is correlated with increased macroevolutionary dispersal. Under the best-fitting trait-dependent DEC + j + t₁₂+ t₂₁ + m₂ model, a single colonization event from Sunda to Sahul during the middle Miocene and two dispersal events from New Guinea and Australia into the Pacific during the late Miocene to early Pliocene were detected. BayesTraits analysis strongly supports a correlation between narrow monocarp width and bright fruit colors. Bird dispersal and the associated traits (narrow monocarp width) may have driven macroevolutionary dispersal for Meiogyne in Australasia–Pacific.

The tribe Trichosporeae is the most species-rich, systemically complex, and morphologically diverse tribe in the Old World Gesneriaceae. It has long been a focal point and a challenge in the phylogeny of Trichosporeae, with frequent unclear relationships and delimitations among a lot of genera. Here, we conducted a molecular phylogenetic analysis by employing nine DNA fragments with a high sampling coverage for key clades in the tribe Trichosporeae. Meanwhile, we carried out a comprehensive morphological and anatomical investigation on vegetative and floral organs in related genera and species, and try to uncover morphological synapomorphies associated with molecular clades. Our results demonstrated a well-supported phylogeny of major clades in the tribe, strongly corroborated by morphological data. We find that some genera, such as Raphiocarpus, Briggsia, and Boeica, are not monophyletic. Based on molecular phylogenetic and morphological analyses, we established five new genera and revived a genus in the tribe Trichosporeae, including Neoraphiocarpus, Anisophyllaea, Hispidopalata, Pseudobriggsia, and Kaiyua with revival of Boeicopsis. We further redefined the genera Raphiocarpus and Briggsiopsis. Our results would deepen our understanding about the phylogeny of the Old World Gesneriaceae.

We present a phylogenetic analysis of benthic ctenophores of the order Platyctenida, sampling all but one genus. Using complete mitochondrial genomes and nuclear ribosomal data and a reassessment of anatomy, our integrated analysis uncovers an unexpectedly close relationship between two unusual members of the Coeloplanidae: Coeloplana (Benthoplana) meteoris and Vallicula multiformis. These two species form a well-supported clade, deriving at or near the base of the tree of Platyctenida, distantly related to other Coeloplana, rendering Coeloplana and Coeloplanidae non-monophyletic. A unique mitochondrial gene order and a tentacle bulb with four extensions are newly identified synapomorphies of this lineage. We elevate the subgenus Benthoplana to the generic level, erect the new family Benthoplanidae for Benthoplana and Vallicula, and provide diagnoses for these taxa and their accepted species. We also show that planktonic Ctenoplana (Diploctena) neritica is the early life stage of Benthoplana meteoris, and suggest that the remaining Ctenoplanidae likely represent early life history stages of Coeloplanidae and perhaps other platyctenes. While both the nuclear ribosomal (18S and 28S) and mitochondrial protein-coding genes suggest a deep phylogenetic divergence between Benthoplanidae and Coeloplanidae, we detect conflicting phylogenetic signal between these markers, suggesting nuclear-mitochondrial discordance, leaving the placement of Tjalfiellidae and Lyroctenidae uncertain.

Pseudoscorpiones are a group of small-sized to medium-sized arachnids under the species-rich Chelicerata. They are found in many terrestrial habitats, normally cryptic, including leaf litter and soil, under tree bark or rocks. The fossil record of pseudoscorpions is mainly composed of species belonging to extinct genera in extant families, with a small number of taxa described from the famous Kachin amber, sometimes referred to as Burmese amber or Burmite (12 species in six families). Here, we describe a well preserved male specimen of pseudoscorpion from mid-Cretaceous Kachin amber, representing the first fossil record of Cheliferidae from Burmese amber. This new taxon, Echinochelifer curvatus gen. & sp. nov., is characterized by elongate tubercle-bearing pedipalps and several trichobothrial features. Based on these, we discuss the systematic placement and palaeoecological implications of the new taxon in Burmese amber.

Many genera were erected without phylogenetic validation in Bittacidae, a cosmopolitan family in Mecoptera, leaving their generic statuses contentious. Here, we investigated the phylogenetic relationships and reconstructed the ancestral states of chromosome numbers and key morphological characters for 26 species in three genera of Bittacidae using an integrative approach combining molecular, cytogenetic, and morphological data. The phylogenetic analyses reveal that all three genera studied are paraphyletic, but cytogenetic evidence supports the generic status of Terrobittacus Tan & Hua with haploid chromosome numbers ≥20. In contrast, the genus Bittacus Latreille, 1805 exhibits an extensive chromosomal variation from n = 8 to n = 22. Ancestral state reconstruction suggests that the diagnostic character of Bicaubittacus Tan & Hua may represent an apomorphy restricted to a few species. The cytogenetic investigation indicates that n = 22 was the ancestral chromosome number in Bittacidae. Chromosome fusions were likely responsible for numerical reduction in chromosomes of Terrobittacus, whereas more complex structural and numerical variations accounted for the chromosome diversity of Bittacus and Bicaubittacus. To satisfactorily resolve the generic problem of Bittacidae, taxon sampling should be greatly expanded at the global scale, and more attention should be paid to the integrative taxonomy.

The peppered moth Biston betularia L., widely distributed across the Northern Hemisphere, represents an ideal organism for exploring phylogeographic patterns 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 Afrocarduus schimperi adopted by the Flora of Tropical East Africa, in fact, comprises seven clearly recognizable species, which we formally reinstate. Unexpectedly, the stemmed Afrocarduus nyassanus was recovered as paraphyletic with Afrocarduus ruwenzoriensis nested within it, probably due to incomplete lineage sorting or hybridization. Additionally, the stemmed Afrocarduus keniensis may represent a complex of cryptic species, and we describe a new stemmed species from southern Ethiopia, Afrocarduus 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.

The genus Phaeolus holds significant economic and ecological value as an important pathogen of coniferous trees. Although species diversity within this genus has been described in recent years, there were limited studies of its origin, evolution, and biogeography. In this study, we collected new specimens from China and the United States, and reconstructed the phylogeny, divergence times, and biogeography of Phaeolus based on internal transcribed spacers (ITS) and nuclear large ribosomal subunit (nLSU) sequences. Phylogenetic analyses identified two new species, Phaeolus himalayanus and Phaeolus occidentiamericanus, one new combination, Phaeolus hispidoides, one synonym, Phaeolus fragilis (treated as Phaeolus schweinitzii), and one new record from China, Phaeolus sharmae. Phaeolus himalayanus is characterized by pileate, imbricate basidiomata, round to irregular pores of two to three per millimeter, abundant gloeoplerous hyphae, mango-shaped to ellipsoid basidiospores (5.5–7 × 4–4.5 µm), and distribution in Xizang of China. Phaeolus occidentiamericanus is characterized by pileate, imbricate basidiomata, round to irregular pores of two to three per millimeter, mango-shaped to ellipsoid basidiospores (6.5–7.8 × 4–5 µm), and distribution in the western United States. Molecular clock analyses indicated that the genus Phaeolus likely originated in the Late Cretaceous, with species divergence occurring between 9–71 Ma. Ancestral state reconstruction suggested that the genus originated in the Himalaya–Hengduan Mountains region and subsequently dispersed to Europe and North America. The earliest host trees of Phaeolus were probably Abies and Pinus, with all known species capable of growing on Pinus, demonstrating a strong host trees preference. Additionally, a key of the genus Phaeolus is added. This study provides a crucial foundation in pathogen control and ecological conservation of this genus in the future.