Search Results (1,584)

In plateau wetlands, the interactions of herbaceous roots with ectorhizosphere soil microorganisms represent an important way to realize their ecological functions. Global change-induced aridification of plateau wetlands has altered long-established functional synergistic relationships between plant roots and ectorhizosphere soil microbes, but we still know little about this phenomenon. In this context, nine typical wetlands with three different moisture statuses were selected from the eastern Tibetan Plateau in this study to analyze the relationships among herbaceous plant root traits and microbial communities and functions. The results revealed that drought significantly inhibited the accumulation of root biomass and surface area as well as the development of root volumes and diameters. Similarly, drought significantly reduced the diversity of ectorhizosphere soil microbial communities and the relative abundances of key phyla of archaea and bacteria. Redundancy analysis revealed that plant root traits and ectorhizosphere soil microbes were equally regulated by soil physicochemical properties. Functional genes related to carbohydrate metabolism were significantly associated with functional traits related to plant root elongation and nutrient uptake. Functional genes related to carbon and energy metabolism were significantly associated with traits related to plant root support and storage. Key genes such as CS,gltA, and G6PD,zwf help to improve the drought resistance and barrenness resistance of plant roots. This study helps to elucidate the synergistic mechanism of plant and soil microbial functions in plateau wetlands under drought stress, and provides a basis for evolutionary research and conservation of wetland ecosystems in the context of global change. Full article

Elucidating the coexistence mechanisms of rapidly diverging species has long been a challenge in evolutionary biology. Genome-wide polymorphic loci are expected to provide insights into the speciation processes of these closely related species. This study focused on seven Chinese sclerophyllous oaks, represented by Quercus spinosa, Quercus aquifolioides, Quercus rehderiana, Quercus guyavifolia, Quercus monimotricha, Quercus semecarpifolia, and Quercus senescens, employing 27,592 single-nucleotide polymorphisms to examine their phylogenetic relationships at the genomic level. Combined with genetic structure analysis, phylogenetic trees revealed that the genetic clustering of individuals was influenced by both geographic distance and ancestral genetic components. Furthermore, this study confirmed the existence of reticulate evolutionary relationships among the species. Frequent gene flow and introgression within the seven species were primarily responsible for the ambiguous interspecies boundaries, with hybridization serving as a major driver of reticulate evolution. Additionally, the seven species exhibited distinct differences in niche occupancy. By reconstructing the climatic adaptability of ancestral taxonomic units, we found that the climatic tolerance of each species displayed differential responses to 19 climatic factors. Consequently, ecological niche differentiation and variations in habitat adaptation contributed to the preservation of species boundaries. This study provides a comprehensive understanding of the speciation processes in rapidly diverging genera and underscores the significance of both genetic and ecological factors in the formation and maintenance of species boundaries. Full article

Complete mitochondrial DNA genome annotation of an ecologically and commercially important fish species Cirrhinus cirrhosus was executed with next-generation sequencing (NGS) for nucleotide and phylogenetic analyses. The findings of this study showed that the Cirrhinus cirrhosus mitochondrial genome contained 16,593 bp, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and a D-loop region. The overall base composition was 32% adenine, 25% thiamine, 16% guanine, and 27% cytosine. This mitochondrial DNA exhibits an AT biasness, with 56% AT content in its genome. Significant fluctuations were identified in the AT and GC skew values of the ND6 gene, indicating that the selection and mutation forces acting on this gene might be different from those acting on other genes. The Ka/Ks ratios of most protein-coding genes were less than 1, indicating very strong natural selection pressure. Phylogenetic analysis of Cirrhinus cirrhosus with Cirrhinus mrigala and Bangana tungting suggested a closer evolutionary relationship among these species, which might have shared a more recent common ancestor. It has been also found that the genera Labeo and Cirrhinus are not monophyletic. Full article

Plant genetics and chemotaxonomic analysis are considered key parameters in understanding evolution, plant diversity and adaptation. Korean Peninsula has a unique biogeographical landscape that supports various aromatic plant species, each with considerable ecological, ethnobotanical, and pharmacological significance. This review aims to provide a comprehensive overview of the chemotaxonomic traits, biological activities, phylogenetic relationships and potential applications of Korean aromatic plants, highlighting their significance in more accurate identification. Chemotaxonomic investigations employing techniques such as gas chromatography mass spectrometry, high-performance liquid chromatography, and nuclear magnetic resonance spectroscopy have enabled the identification of essential oils and specialized metabolites that serve as valuable taxonomic and diagnostic markers. These chemical traits play essential roles in species delimitation and in clarifying interspecific variation. The biological activities of selected taxa are reviewed, with emphasis on antimicrobial, antioxidant, anti-inflammatory, and cytotoxic effects, supported by bioassay-guided fractionation and compound isolation. In parallel, recent advances in phylogenetic reconstruction employing DNA barcoding, internal transcribed spacer regions, and chloroplast genes such as rbcL and matK are examined for their role in clarifying taxonomic uncertainties and inferring evolutionary lineages. Overall, the search period was from year 2001 to 2025 and total of 268 records were included in the study. By integrating phytochemical profiling, pharmacological evidence, and molecular systematics, this review highlights the multifaceted significance of Korean endemic aromatic plants. The conclusion highlights the importance of multidisciplinary approaches including metabolomics and phylogenomics in advancing our understanding of species diversity, evolutionary adaptation, and potential applications. Future research directions are proposed to support conservation efforts. Full article

Systematic reviews are a cornerstone of evidence-based research, providing comprehensive summaries of existing studies to answer specific research questions. This article offers a detailed guide to conducting high-quality systematic reviews in biology, health and social sciences. It outlines key steps, including developing and registering a protocol, designing comprehensive search strategies, and selecting studies through a screening process. The article emphasizes the importance of accurate data extraction and the use of validated tools to assess the risk of bias across different study designs. Both meta-analysis (quantitative approach) and narrative synthesis (qualitative approach) are discussed in detail. The guide also highlights the use of frameworks, such as GRADE, to assess the certainty of evidence and provides recommendations for clear and transparent reporting in line with the PRISMA 2020 guidelines. This paper aims to adapt and translate evidence-based review principles, commonly applied in clinical research, into the context of biological sciences. By highlighting domain-specific methodologies, challenges, and resources, we provide tailored guidance for researchers in ecology, molecular biology, evolutionary biology, and related fields in order to conduct transparent and reproducible evidence syntheses. Full article

Chromosome rearrangements during plant evolution can lead to alterations in genome structure and gene function, thereby influencing species adaptation and evolutionary processes. Gymnosperms, as an ancient group of plants, offer valuable insights into the morphological, physiological, and ecological characteristics of early terrestrial flora. The reconstruction of ancestral karyotypes in gymnosperms may provide critical clues for understanding their evolutionary history. In this study, we inferred the ancestral gymnosperm karyotype (AGK), which comprises 12 chromosomes, and conducted a collinearity analysis with existing gymnosperm genomes. Our findings indicate that chromosome numbers have remained remarkably stable throughout the evolution of gymnosperms. For species with multiplied chromosome numbers, such as gnetophytes, weak collinearities with the AGK were observed. Comparisons between the AGK and gnetophyte genomes revealed a biased pattern regarding retained duplication blocks. Furthermore, our analysis of transposable elements in Welwitschia mirabilis identified enriched regions containing LINE-1 retrotransposons within the syntenic blocks. Syntenic analysis between the AGK and angiosperms also demonstrated a biased distribution across chromosomes. These results provide a fundamental resource for further characterization of chromosomal evolution in gymnosperms. Full article

Halictidae, as a major pollinator family in bees, has significant ecological value. However, the insufficient molecular data for this group has limited our understanding of the evolutionary history of this group. Herein, we newly sequenced and assembled four mitogenomes of Halictidae, including three species of Nomiinae and one species of Rophitinae. We analyzed the characters of the newly obtained mitogenomes, including nucleotide composition, sequence length, and gene rearrangements. The length of the newly sequenced mitogenomes ranged from 16,492 to 21,192 bp, and all newly obtained mitogenomes contained 22 tRNAs, 13 protein-coding genes, two rRNAs, and one control region. Their AT content (%) ranged from 82.55 to 86.44. Relative synonymous codon usage analysis showed that UUU, UUA, and AUU were the preferred codons. The relative synonymous codon usage > 2 of mostly newly sequenced species was as follows: UUA > UCA > CGA. All newly obtained mitogenomes show gene rearrangement; we found five gene rearrangement patterns in total. Notably, ND4-trnP-ND4L-trnT was the first reported gene rearrangement pattern in bees. In addition, we reconstructed the phylogenetic relationships of Halictidae based on 10 species (eight ingroups and two outgroups), using Bayesian Inference and Maximum Likelihood approaches. Phylogenetic analysis showed that Rophitinae was the basal group within Halictidae. Full article

China’s southwestern karst landscapes support remarkable cavefish diversity, especially within Sinocyclocheilus, the world’s largest cavefish genus. Using integrative taxonomic methods, we describe Sinocyclocheilus wanlanensis sp. nov., found in a subterranean river in Guizhou Province. This species lacks horn-like cranial structures; its eyes are either reduced to a dark spot or absent. It possesses a pronounced nuchal hump and a forward-protruding, duckbill-shaped head. Morphometric analysis of 28 individuals from six species shows clear separation from related taxa. Nano-CT imaging reveals distinct vertebral and cranial features. Phylogenetic analyses of mitochondrial cytb and ND4 genes place S. wanlanensis within S. angularis group as sister to S. bicornutus, with p-distances of 1.7% (cytb) and 0.7% (ND4), consistent with sister-species patterns within the genus. Sinocyclocheilus wanlanensis is differentiated from S. bicornutus by its eyeless or degenerate-eye condition and lack of bifurcated horns. It differs from S. zhenfengensis, its morphologically closest species, in having degenerate or absent eyes, shorter maxillary barbels, and pelvic fins that reach the anus. The combination of morphological and molecular evidence supports its recognition as a distinct species. Accurate documentation of such endemic and narrowly distributed taxa is important for conservation and for understanding speciation in cave habitats. Full article

The Millard’s rat (Dacnomys millardi), a threatened murid endemic to Southeast Asian montane rainforests and the sole member of its monotypic genus, faces escalating endangered risks as a Near Threatened species in China’s Biodiversity Red List. This ecologically specialized rodent exhibits diagnostic morphological adaptations—hypertrophied upper molars and cryptic pelage—that underpin niche differentiation in undisturbed tropical/subtropical forests. Despite its evolutionary distinctiveness, the conservation prioritization given to Dacnomys is hindered due to a deficiency of data and unresolved phylogenetic relationships. Here, we integrated morphological analyses with the first complete mitogenome (16,289 bp in size; no structural rearrangements) of D. millardi to validate its phylogenetic placement within the subfamily Murinae and provide novel insights into genetic diversity erosion. Bayesian and maximum likelihood phylogenies robustly supported Dacnomys as sister to Leopoldamys (PP = 1.0; BS = 100%), with an early Pliocene divergence (~4.8 Mya, 95% HPD: 3.65–5.47 Mya). Additionally, based on its basal phylogenetic position within Murinae, we propose reclassifying Micromys from Rattini to the tribe Micromyini. Codon usage bias analyses revealed pervasive purifying selection (Ka/Ks < 1), constraining mitogenome evolution. Genetic diversity analyses showed low genetic variation (CYTB: π = 0.0135 ± 0.0023; COX1: π = 0.0101 ± 0.0025) in fragmented populations. We propose three new insights into this genetic diversity erosion. (1) Evolutionary constraints: genome-wide evolutionary conservation and shallow evolutionary history (~4.8 Mya) limited mutation accumulation. (2) Anthropogenic pressures: deforestation-driven fragmentation of habitats (>20,000 km²/year loss since 2000) has reduced effective population size, exacerbating genetic drift. (3) Ecological specialization: long-term adaptation to stable niches favored genomic optimization over adaptive flexibility. These findings necessitate suitable conservation action by enforcing protection of core habitats to prevent deforestation-driven population collapses and advocating IUCN reclassification of D. millardi from Data Deficient to Near Threatened. Full article

Amidst the intensification of global climate change and the increasing impacts of human activities, ecosystem patterns and processes have undergone substantial transformations. The distribution and evolutionary dynamics of mountain ecosystems have become a focal point in ecological research. The Surkhan River Basin is located in the transitional zone between the arid inland regions of Central Asia and the mountain systems, where its unique physical and geographical conditions have shaped distinct patterns of vertical zonation. Utilizing Landsat imagery, this study applies a hierarchical classification approach to derive land cover classifications within the Surkhan River Basin. By integrating the NDVI (normalized difference vegetation index) and DEM (digital elevation model (30 m SRTM)), an “NDVI-DEM-Land Cover” scatterplot is constructed to analyze zonation characteristics from 1980 to 2020. The 2020 results indicate that the elevation boundary between the temperate desert and mountain grassland zones is 1100 m, while the boundary between the alpine cushion vegetation zone and the ice/snow zone is 3770 m. Furthermore, leveraging DEM and LST (land surface temperature) data, a potential energy analysis model is employed to quantify potential energy differentials between adjacent zones, enabling the identification of ecological transition areas. The potential energy analysis further refines the transition zone characteristics, indicating that the transition zone between the temperate desert and mountain grassland zones spans 1078–1139 m with a boundary at 1110 m, while the transition between the alpine cushion vegetation and ice/snow zones spans 3729–3824 m with a boundary at 3768 m. Cross-validation with scatterplot results confirms that the scatterplot analysis effectively delineates stable zonation boundaries with strong spatiotemporal consistency. Moreover, the potential energy analysis offers deeper insights into ecological transition zones, providing refined boundary identification. The integration of these two approaches addresses the dimensional limitations of traditional vertical zonation studies, offering a transferable methodological framework for mountain ecosystem research. Full article

Stable isotope analysis has become a key tool in paleontology, providing insights into ancient diets, ecosystems, climates, and environmental shifts. Despite the growing importance of isotopic studies in South America, no comprehensive bibliometric review has been conducted until now. This study addresses that gap, analyzing the development of the field over the past thirty years. Our results show a rapidly expanding discipline, especially in the last five years, with increasing publication rates and participation from South American researchers, particularly in Brazil and Argentina. However, the analysis also reveals persistent biases: notably, a strong focus on the Quaternary period, which limits broader evolutionary interpretations. Keyword co-occurrence points to dominant themes such as paleodiet, paleoecology, and megafaunal extinction, while highlighting new trends like ecological niche modeling and nitrogen isotope applications. The co-authorship network reflects high levels of collaboration, particularly with Spain and the United States. A marked gender imbalance in authorship is also evident, calling attention to the need for greater inclusivity. This review emphasizes the importance of addressing taxonomic and temporal gaps, strengthening interdisciplinary and international networks, and promoting equity in order to ensure the continued growth and global relevance of isotopic paleontology in South America. Full article

Background/Objectives: Scutiger ningshanensis (Fang, 1985) is an endemic Chinese amphibian species within the genus Scutiger (Megophryidae). Despite its ecological significance, its mitochondrial genome architecture and evolutionary relationships remain poorly understood. Given the high structural variability in Megophryidae mitogenomes and unresolved phylogenetic patterns in Scutiger, this study aims to (1) characterize the complete mitogenome of S. ningshanensis, (2) analyze its molecular evolution, and (3) clarify its phylogenetic position and divergence history within Megophryidae. Methods: The complete mitochondrial genome was sequenced and annotated, followed by analyses of nucleotide composition, codon usage bias, and selection pressures (Ka/Ks ratios). Secondary structures of rRNAs and tRNAs were predicted, and phylogenetic relationships were reconstructed using maximum likelihood and Bayesian methods. Divergence times were estimated using molecular clock analysis. Results: The mitogenome of S. ningshanensis is 17,282 bp long, encoding 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and a control region, with a notable AT bias (61.05%) with nucleotide compositions of T (32.51%), C (24.64%), G (14.3%), and A (28.54%). All tRNAs exhibited cloverleaf structures except trnS1, which lacked a DHU stem. Phylogenetic analysis confirmed the monophyly of Scutiger, forming a sister clade to Oreolalax and Leptobrachium, and that S. ningshanensis and S. liubanensis are sister species with a close evolutionary relationship. Positive selection was detected in Atp8 (Ka/Ks > 1), suggesting adaptation to plateau environments, while other PCGs underwent purifying selection (Ka/Ks < 1). Divergence time estimation placed the origin of Megophryidae at~47.97 MYA (Eocene), with S. ningshanensis diverging~32.67 MYA (Oligocene). Conclusions: This study provides the first comprehensive mitogenomic characterization of S. ningshanensis, revealing its evolutionary adaptations and phylogenetic placement. The findings enhance our understanding of Megophryidae’s diversification and offer a genomic foundation for future taxonomic and conservation studies. Full article

Amdoparvoviruses, encompassing the well-characterized Aleutian mink disease viruses (AMDV) as well as less investigated viruses infecting both captive and wild animals, are important carnivoran viruses that are significant pathogens in the mink farming industry. We investigated the molecular epidemiology of amdoparvoviruses among Danish wildlife. Spleen samples from 118 animals of seven carnivoran species were screened with a pan-amdoparvovirus PCR, and the identified viruses were molecularly characterized. In one of five European badgers (Meles meles), we identified an AMDV-3 strain whose ancestors were likely of farmed mink origin. This virus was last reported on a mink farm in 2002, demonstrating how farm-derived viruses have established themselves among wildlife. We also discovered and fully characterized a novel virus found in five of 81 (6.2%) foxes (Vulpes vulpes) and one of five badgers (20.0%), which we named fox and badger amdoparvovirus 1 (FBAV-1). FBAV-1 fulfills the criteria for classification as a novel species and phylogenetically is positioned as an intermediate between the North American and Eurasian amdoparvoviral clades. This study provides baseline data and expands our understanding of amdoparvoviral ecology. Further studies including more animals across diverse geographic areas are warranted to clarify amdoparvovirus epidemiology, spread, cross-species transmission, epidemic potential, and evolutionary paths. Full article

White-Nose Syndrome (WNS) has devastated insectivorous bat populations, particularly in North America, leading to severe ecological and economic consequences. Despite extensive research, many aspects of the evolutionary history, mitochondrial genome organization, and metabolic adaptations of its etiological agent, Pseudogymnoascus destructans, remain unexplored. Here, we present a multi-scale genomic analysis integrating pangenome reconstruction, phylogenetic inference, Bayesian divergence dating, comparative mitochondrial genomics, and refined functional annotation. We show that P. destructans exhibits extensive mitochondrial genome rearrangements absent in its nonpathogenic relatives from the Leotiomycetes class, suggesting a potential link between mitochondrial evolution and pathogenic adaptation. Our divergence dating analysis reveals that P. destructans separated from its Antarctic relatives approximately 141 million years ago, before adapting to bat hibernacula in the Northern Hemisphere. Additionally, our refined functional annotation significantly expands the known functional landscape of P. destructans, revealing an extensive repertoire of previously uncharacterized proteins involved in carbohydrate metabolism and secondary metabolite biosynthesis—key processes that likely contribute to its pathogenic success. By providing new insights into the genomic basis of P. destructans adaptation and pathogenicity, our study refines the evolutionary framework of this fungal pathogen and creates the foundation for future research on WNS mitigation strategies. Full article

The interconnections among water, energy, and food (WEF) systems are growing increasingly complex, making it essential to understand their evolutionary mechanisms and coordination barriers to enhance regional resilience and sustainability. In this study, we investigated the WEF system in Northeast China by constructing a comprehensive indicator system encompassing resource endowment and utilization efficiency. The coupling coordination degree (CCD) of the WEF system was quantitatively assessed from 2001 to 2022. An obstacle degree model was employed to identify key constraints, while grey relational analysis was used to evaluate the driving influence of individual indicators. Furthermore, a co-evolution model based on logistic growth and competition–cooperation dynamics was developed to simulate system interactions. The results reveal the following: (1) the regional WEF-CCD increased from 0.627 in 2001 to 0.769 in 2022, reaching the intermediate coordination level, with the CCDs of the food, water, and energy subsystems rising from 0.39 to 0.62, 0.38 to 0.60, and 0.40 to 0.55, respectively, highlighting that the food subsystem had the most stable and significant improvement; (2) Jilin Province attained the highest WEF-CCD, 0.850, in 2022, while that for Heilongjiang remained the lowest, at 0.715, indicating substantial interprovincial disparities; (3) key indicators, such as food self-sufficiency rate, electricity generation, and ecological water use, functioned as both core constraints and major drivers of system performance; (4) co-evolution modeling revealed that the food subsystem exhibited the fastest growth, followed by water and energy (${\alpha }_3$ >${ \alpha }_1$ > ${ \alpha }_2$ > 0), with mutual promotion between water and energy subsystems and inhibitory effects from the food subsystem, ultimately converging toward a stable equilibrium state; and (5) interprovincial co-evolution modeling indicated that Jilin leads in WEF system development, followed by Liaoning and Heilongjiang, with predominantly cooperative interactions among provinces driving convergence toward a stable and coordinated equilibrium despite structural asymmetries. This study proposes a transferable, multi-method analytical framework for evaluating WEF coordination, offering practical insights into bottlenecks, key drivers, and co-evolutionary dynamics for sustainable resource governance. Full article